From 97e152d4e5d5324b4e8612afe83eef1c91f3328e Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 14:13:38 +0100 Subject: [PATCH 01/36] correct eggnog mapper version bug while not use --- bin/scrape_software_versions.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 86f979f..6b74a59 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -2,6 +2,7 @@ from __future__ import print_function from collections import OrderedDict import re +import os regexes = { 'metagWGS': ['v_pipeline.txt', r"(\S+)"], @@ -49,11 +50,12 @@ results['Eggnog-Mapper'] = '<span style="color:#999999;\">N/A</span>' # Search each file using its regex for k, v in regexes.items(): - with open(v[0]) as x: - versions = x.read() - match = re.search(v[1], versions) - if match: - results[k] = "v{}".format(match.group(1)) + if os.path.exists(v[0]): + with open(v[0]) as x: + versions = x.read() + match = re.search(v[1], versions) + if match: + results[k] = "v{}".format(match.group(1)) # Remove software set to false in results for k in results: -- GitLab From 820a630e34053129857b16a7bf49b9bbaee39bb9 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:54:20 +0100 Subject: [PATCH 02/36] correct host + taxonomy_dir paths --- functional_tests/expected_processes_HiFi.tsv | 4 +-- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index 4555d12..e278d4c 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 1f0ab4c..9d09ccf 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 -- GitLab From 2cf7e07b329788872da1befee222ed5c117d672a Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 03/36] update docs + add environement variables --- docs/usage.md | 8 +++--- functional_tests/README.md | 42 +++++++++++++++++++++--------- functional_tests/launch_example.sh | 2 +- 3 files changed, 35 insertions(+), 17 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 2644fc8..2237db7 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,9 +10,9 @@ > ``` > sample,fastq_1,fastq_2 - > a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz - > a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz - > c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz + > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz + > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz + > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz > ``` 4. Run a basic script: @@ -33,7 +33,7 @@ > nextflow run -profile test_genotoul_workq metagwgs/main.nf \ > --type 'SR' \ > --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \ - > --skip_host_filter --skip_kaiju + > --skip_host_filter --skip_kaiju --stop_at_clean > ``` > **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3. diff --git a/functional_tests/README.md b/functional_tests/README.md index 387ff1c..4d56af4 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -5,18 +5,17 @@ 1. Install metagwgs as described here: [installation doc](../docs/installation.md) 2. Get datasets: two datasets are currently available for these functional tests at `https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git` - Replace "\<dataset\>" with either "small" or "mag": ``` - git clone --branch <dataset> git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git + git clone git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git or - wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/archive/<dataset>/metagwgs-test-datasets-<dataset>.tar.gz + wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git ``` -3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-10-19.tar.gz) and decompress its contents in any folder. This archive contains data banks for: +3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz) and decompress its contents in any folder. This archive contains data banks for: - **Kaiju** (_kaijudb_refseq_2020-05-25_) - **Diamond** (_refseq_bacteria_2021-05-20_) - - **NCBI Taxonomy** (_taxonomy_2021-08-23_) + - **NCBI Taxonomy** (_taxonomy_2021-12-7_ ) - **Eggnog Mapper** (_eggnog-mapper-2.0.4-rf1_) @@ -30,15 +29,34 @@ To launch functional tests, you need to be located at the root of the folder whe - by providing the results folder of a pipeline already exectuted ``` cd test_folder -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results +export METAG_PATH="/path/to/sources" +export DATASET="/path/to/metagwgs-test-datasets" +python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results ``` - by providing a script which will launch the nextflow pipeline [see example](./launch_example.sh) (this example is designed for the "small" dataset with --min_contigs_cpm>1000, using slurm) -``` -mkdir test_folder -cd test_folder -cp <metagwgs-src>/functional_tests/launch_example.sh ./ -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results --script launch_example.sh -``` + + 1. create working directory + ``` + mkdir test_folder + cd test_folder + ``` + + 2.set enviroment variables and load module + + ``` + export METAG_PATH="/path/to/sources" + export DATASET="/path/to/metagwgs-test-datasets" + export DATABANK="/path/to/FT_banks_2021-10-19" + export EGGNOG_DB="$DATABANK/eggnog-mapper-2.0.4-rf1/data" + module load system/Python-3.7.4 + ``` + + 3.launch functional test + + ``` + cp $METAG_PATH/functional_tests/launch_example.sh ./ + python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results --script launch_example.sh + ``` >**NOTE: more information on the command used to produce each dataset in [small](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/small) and [mag](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/mag) READMEs** diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 3a95935..7d69bdd 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq main.nf --type 'SR' --input 'metagwgs-test-datasets/small/input/samplesheet.csv' --host_fasta 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir 'FT_banks_2021-10-19/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank 'FT_banks_2021-10-19/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir 'FT_banks_2021-10-19/eggnog-mapper-2.0.4-rf1/data' --taxonomy_dir 'FT_banks_2021-10-19/taxonomy_2021-08-23' --stop_at_clean -with-report -with-timeline -with-trace -with-dag" \ No newline at end of file + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 5a626c908acc874ae88acb3329a4f52f642b3c5d Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 10:44:00 +0100 Subject: [PATCH 04/36] remove diamond bank necessity when not use --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 46bccb4..9a05ad1 100644 --- a/main.nf +++ b/main.nf @@ -166,7 +166,7 @@ workflow { skip_clean = true } - if ( !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { + if ( !(params.stop_at_clean) && !(params.stop_at_assembly) && !(params.stop_at_filtering) && !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { exit 1, "You must specify --stop_at_structural_annot or specify a diamond bank with --diamond_bank" } header = getAndCheckHeader() -- GitLab From 702803ceb01eebc0445e03298f4713511bb5489d Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 14:13:38 +0100 Subject: [PATCH 05/36] correct eggnog mapper version bug while not use --- bin/scrape_software_versions.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 86f979f..6b74a59 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -2,6 +2,7 @@ from __future__ import print_function from collections import OrderedDict import re +import os regexes = { 'metagWGS': ['v_pipeline.txt', r"(\S+)"], @@ -49,11 +50,12 @@ results['Eggnog-Mapper'] = '<span style="color:#999999;\">N/A</span>' # Search each file using its regex for k, v in regexes.items(): - with open(v[0]) as x: - versions = x.read() - match = re.search(v[1], versions) - if match: - results[k] = "v{}".format(match.group(1)) + if os.path.exists(v[0]): + with open(v[0]) as x: + versions = x.read() + match = re.search(v[1], versions) + if match: + results[k] = "v{}".format(match.group(1)) # Remove software set to false in results for k in results: -- GitLab From 9bbcb27268b5e90df5ebb885008dbf8b54bfce90 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:54:20 +0100 Subject: [PATCH 06/36] correct host + taxonomy_dir paths --- functional_tests/expected_processes_HiFi.tsv | 4 +-- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index 4555d12..e278d4c 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 1f0ab4c..9d09ccf 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 -- GitLab From c343d7af71e7b2aec7e8b8b865a3202e6d92b16a Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 07/36] update docs + add environement variables --- docs/usage.md | 8 +++--- functional_tests/README.md | 42 +++++++++++++++++++++--------- functional_tests/launch_example.sh | 2 +- 3 files changed, 35 insertions(+), 17 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 924523d..a476cfb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,9 +10,9 @@ > ``` > sample,fastq_1,fastq_2 - > a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz - > a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz - > c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz + > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz + > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz + > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz > ``` 4. Run a basic script: @@ -33,7 +33,7 @@ > nextflow run -profile test_genotoul_workq metagwgs/main.nf \ > --type 'SR' \ > --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \ - > --skip_host_filter --skip_kaiju + > --skip_host_filter --skip_kaiju --stop_at_clean > ``` > **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3. diff --git a/functional_tests/README.md b/functional_tests/README.md index 387ff1c..4d56af4 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -5,18 +5,17 @@ 1. Install metagwgs as described here: [installation doc](../docs/installation.md) 2. Get datasets: two datasets are currently available for these functional tests at `https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git` - Replace "\<dataset\>" with either "small" or "mag": ``` - git clone --branch <dataset> git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git + git clone git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git or - wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/archive/<dataset>/metagwgs-test-datasets-<dataset>.tar.gz + wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git ``` -3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-10-19.tar.gz) and decompress its contents in any folder. This archive contains data banks for: +3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz) and decompress its contents in any folder. This archive contains data banks for: - **Kaiju** (_kaijudb_refseq_2020-05-25_) - **Diamond** (_refseq_bacteria_2021-05-20_) - - **NCBI Taxonomy** (_taxonomy_2021-08-23_) + - **NCBI Taxonomy** (_taxonomy_2021-12-7_ ) - **Eggnog Mapper** (_eggnog-mapper-2.0.4-rf1_) @@ -30,15 +29,34 @@ To launch functional tests, you need to be located at the root of the folder whe - by providing the results folder of a pipeline already exectuted ``` cd test_folder -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results +export METAG_PATH="/path/to/sources" +export DATASET="/path/to/metagwgs-test-datasets" +python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results ``` - by providing a script which will launch the nextflow pipeline [see example](./launch_example.sh) (this example is designed for the "small" dataset with --min_contigs_cpm>1000, using slurm) -``` -mkdir test_folder -cd test_folder -cp <metagwgs-src>/functional_tests/launch_example.sh ./ -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results --script launch_example.sh -``` + + 1. create working directory + ``` + mkdir test_folder + cd test_folder + ``` + + 2.set enviroment variables and load module + + ``` + export METAG_PATH="/path/to/sources" + export DATASET="/path/to/metagwgs-test-datasets" + export DATABANK="/path/to/FT_banks_2021-10-19" + export EGGNOG_DB="$DATABANK/eggnog-mapper-2.0.4-rf1/data" + module load system/Python-3.7.4 + ``` + + 3.launch functional test + + ``` + cp $METAG_PATH/functional_tests/launch_example.sh ./ + python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results --script launch_example.sh + ``` >**NOTE: more information on the command used to produce each dataset in [small](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/small) and [mag](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/mag) READMEs** diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 3a95935..7d69bdd 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq main.nf --type 'SR' --input 'metagwgs-test-datasets/small/input/samplesheet.csv' --host_fasta 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir 'FT_banks_2021-10-19/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank 'FT_banks_2021-10-19/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir 'FT_banks_2021-10-19/eggnog-mapper-2.0.4-rf1/data' --taxonomy_dir 'FT_banks_2021-10-19/taxonomy_2021-08-23' --stop_at_clean -with-report -with-timeline -with-trace -with-dag" \ No newline at end of file + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From db4d7d20063c9b56554a8635544ec29e477f0ffb Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 10:44:00 +0100 Subject: [PATCH 08/36] remove diamond bank necessity when not use --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 46bccb4..9a05ad1 100644 --- a/main.nf +++ b/main.nf @@ -166,7 +166,7 @@ workflow { skip_clean = true } - if ( !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { + if ( !(params.stop_at_clean) && !(params.stop_at_assembly) && !(params.stop_at_filtering) && !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { exit 1, "You must specify --stop_at_structural_annot or specify a diamond bank with --diamond_bank" } header = getAndCheckHeader() -- GitLab From d0f68b10971e5dbcc8b183bc26ba86ba2d02e735 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 13:02:29 +0100 Subject: [PATCH 09/36] update functional_tests with new profiles --- functional_tests/README.md | 2 +- functional_tests/expected_processes_HiFi.tsv | 10 +++--- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- functional_tests/launch_example.sh | 2 +- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/functional_tests/README.md b/functional_tests/README.md index 4d56af4..25f1b36 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -150,7 +150,7 @@ To use it : ``` cut -f 1 $METAG_PATH/functional_tests/expected_processes_sr.tsv | tail -n +2 > $OUTDIR/cmd_sr.sh ``` - > the commands use profile `test_genotoul_workq` + > the commands use profile `test,genotoul` - replace path in the samplesheet : ``` sed -i -e "s,\$DATASET,$DATASET,g" $DATASET/small/input/samplesheet.csv diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index e278d4c..cf9eacf 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 9d09ccf..4f146c8 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 7d69bdd..0905b24 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 5eb82430fb12fdbfeb8e93e198398e912f025011 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 16:54:03 +0100 Subject: [PATCH 10/36] Check gff validity (issue : check point prokka) --- modules/prokka.nf | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/prokka.nf b/modules/prokka.nf index 44c3475..bb2c305 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -7,11 +7,18 @@ process PROKKA { output: tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results path "PROKKA_${sampleId}/${sampleId}.txt", emit: report + path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results script: """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk + + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + then + rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + fi """ } -- GitLab From 819c6301ff906158b2fd62f70698013234f7d4a8 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Thu, 13 Jan 2022 09:46:12 +0100 Subject: [PATCH 11/36] replace bedtools bamtofastq with samtools fastq (direct fastq.gz) --- modules/prokka.nf | 7 +------ modules/reads_deduplication.nf | 3 +-- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/modules/prokka.nf b/modules/prokka.nf index bb2c305..d2341c3 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -13,12 +13,7 @@ process PROKKA { """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk - - gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - then - rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - fi + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff """ } diff --git a/modules/reads_deduplication.nf b/modules/reads_deduplication.nf index 72b8ff3..c675efd 100644 --- a/modules/reads_deduplication.nf +++ b/modules/reads_deduplication.nf @@ -24,8 +24,7 @@ process READS_DEDUPLICATION { samtools idxstats ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.idxstats samtools flagstat ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.flagstat samtools sort -n -o ${sampleId}.filtered.sort.bam ${sampleId}.filtered.bam - bedtools bamtofastq -i ${sampleId}.filtered.sort.bam -fq ${sampleId}_R1_dedup.fastq -fq2 ${sampleId}_R2_dedup.fastq - gzip ${sampleId}_R1_dedup.fastq ; gzip ${sampleId}_R2_dedup.fastq + samtools fastq -N -1 ${sampleId}_R1_dedup.fastq.gz -2 ${sampleId}_R2_dedup.fastq.gz ${sampleId}.filtered.sort.bam rm ${sampleId}.sort.bam rm ${sampleId}.fixmate.bam rm ${sampleId}.fixmate.positionsort.bam -- GitLab From df0479a16d85f14fe7a8cfb6a8d23db47287049a Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 14:13:38 +0100 Subject: [PATCH 12/36] correct eggnog mapper version bug while not use --- bin/scrape_software_versions.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 86f979f..6b74a59 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -2,6 +2,7 @@ from __future__ import print_function from collections import OrderedDict import re +import os regexes = { 'metagWGS': ['v_pipeline.txt', r"(\S+)"], @@ -49,11 +50,12 @@ results['Eggnog-Mapper'] = '<span style="color:#999999;\">N/A</span>' # Search each file using its regex for k, v in regexes.items(): - with open(v[0]) as x: - versions = x.read() - match = re.search(v[1], versions) - if match: - results[k] = "v{}".format(match.group(1)) + if os.path.exists(v[0]): + with open(v[0]) as x: + versions = x.read() + match = re.search(v[1], versions) + if match: + results[k] = "v{}".format(match.group(1)) # Remove software set to false in results for k in results: -- GitLab From e34af630ebc3b4d2a7ed04456727c74be6ac7f6d Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:54:20 +0100 Subject: [PATCH 13/36] correct host + taxonomy_dir paths --- functional_tests/expected_processes_HiFi.tsv | 4 +-- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index 4555d12..e278d4c 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 1f0ab4c..9d09ccf 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 -- GitLab From 96af8f1f6c65851c15232df8420947c559c665db Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 14/36] update docs + add environement variables --- docs/usage.md | 8 +++--- functional_tests/README.md | 42 +++++++++++++++++++++--------- functional_tests/launch_example.sh | 2 +- 3 files changed, 35 insertions(+), 17 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 924523d..a476cfb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,9 +10,9 @@ > ``` > sample,fastq_1,fastq_2 - > a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz - > a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz - > c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz + > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz + > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz + > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz > ``` 4. Run a basic script: @@ -33,7 +33,7 @@ > nextflow run -profile test_genotoul_workq metagwgs/main.nf \ > --type 'SR' \ > --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \ - > --skip_host_filter --skip_kaiju + > --skip_host_filter --skip_kaiju --stop_at_clean > ``` > **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3. diff --git a/functional_tests/README.md b/functional_tests/README.md index 387ff1c..4d56af4 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -5,18 +5,17 @@ 1. Install metagwgs as described here: [installation doc](../docs/installation.md) 2. Get datasets: two datasets are currently available for these functional tests at `https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git` - Replace "\<dataset\>" with either "small" or "mag": ``` - git clone --branch <dataset> git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git + git clone git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git or - wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/archive/<dataset>/metagwgs-test-datasets-<dataset>.tar.gz + wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git ``` -3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-10-19.tar.gz) and decompress its contents in any folder. This archive contains data banks for: +3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz) and decompress its contents in any folder. This archive contains data banks for: - **Kaiju** (_kaijudb_refseq_2020-05-25_) - **Diamond** (_refseq_bacteria_2021-05-20_) - - **NCBI Taxonomy** (_taxonomy_2021-08-23_) + - **NCBI Taxonomy** (_taxonomy_2021-12-7_ ) - **Eggnog Mapper** (_eggnog-mapper-2.0.4-rf1_) @@ -30,15 +29,34 @@ To launch functional tests, you need to be located at the root of the folder whe - by providing the results folder of a pipeline already exectuted ``` cd test_folder -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results +export METAG_PATH="/path/to/sources" +export DATASET="/path/to/metagwgs-test-datasets" +python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results ``` - by providing a script which will launch the nextflow pipeline [see example](./launch_example.sh) (this example is designed for the "small" dataset with --min_contigs_cpm>1000, using slurm) -``` -mkdir test_folder -cd test_folder -cp <metagwgs-src>/functional_tests/launch_example.sh ./ -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results --script launch_example.sh -``` + + 1. create working directory + ``` + mkdir test_folder + cd test_folder + ``` + + 2.set enviroment variables and load module + + ``` + export METAG_PATH="/path/to/sources" + export DATASET="/path/to/metagwgs-test-datasets" + export DATABANK="/path/to/FT_banks_2021-10-19" + export EGGNOG_DB="$DATABANK/eggnog-mapper-2.0.4-rf1/data" + module load system/Python-3.7.4 + ``` + + 3.launch functional test + + ``` + cp $METAG_PATH/functional_tests/launch_example.sh ./ + python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results --script launch_example.sh + ``` >**NOTE: more information on the command used to produce each dataset in [small](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/small) and [mag](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/mag) READMEs** diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 3a95935..7d69bdd 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq main.nf --type 'SR' --input 'metagwgs-test-datasets/small/input/samplesheet.csv' --host_fasta 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir 'FT_banks_2021-10-19/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank 'FT_banks_2021-10-19/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir 'FT_banks_2021-10-19/eggnog-mapper-2.0.4-rf1/data' --taxonomy_dir 'FT_banks_2021-10-19/taxonomy_2021-08-23' --stop_at_clean -with-report -with-timeline -with-trace -with-dag" \ No newline at end of file + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 80566ab3a1d9311e8e9d2a2706d9b94f3775dacb Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 10:44:00 +0100 Subject: [PATCH 15/36] remove diamond bank necessity when not use --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 46bccb4..9a05ad1 100644 --- a/main.nf +++ b/main.nf @@ -166,7 +166,7 @@ workflow { skip_clean = true } - if ( !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { + if ( !(params.stop_at_clean) && !(params.stop_at_assembly) && !(params.stop_at_filtering) && !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { exit 1, "You must specify --stop_at_structural_annot or specify a diamond bank with --diamond_bank" } header = getAndCheckHeader() -- GitLab From 9311b5c435dd8a3fe521cde6c45d3e7ed91b330a Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 13:02:29 +0100 Subject: [PATCH 16/36] update functional_tests with new profiles --- functional_tests/README.md | 2 +- functional_tests/expected_processes_HiFi.tsv | 10 +++--- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- functional_tests/launch_example.sh | 2 +- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/functional_tests/README.md b/functional_tests/README.md index 4d56af4..25f1b36 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -150,7 +150,7 @@ To use it : ``` cut -f 1 $METAG_PATH/functional_tests/expected_processes_sr.tsv | tail -n +2 > $OUTDIR/cmd_sr.sh ``` - > the commands use profile `test_genotoul_workq` + > the commands use profile `test,genotoul` - replace path in the samplesheet : ``` sed -i -e "s,\$DATASET,$DATASET,g" $DATASET/small/input/samplesheet.csv diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index e278d4c..cf9eacf 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 9d09ccf..4f146c8 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 7d69bdd..0905b24 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From aec8331d0787656b960147f1734458881ca6a4a0 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 16:54:03 +0100 Subject: [PATCH 17/36] Check gff validity (issue : check point prokka) --- modules/prokka.nf | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/prokka.nf b/modules/prokka.nf index 44c3475..bb2c305 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -7,11 +7,18 @@ process PROKKA { output: tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results path "PROKKA_${sampleId}/${sampleId}.txt", emit: report + path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results script: """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk + + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + then + rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + fi """ } -- GitLab From 06beeb7669392ac6b56c596db1bedbbd36979d25 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Thu, 13 Jan 2022 09:46:12 +0100 Subject: [PATCH 18/36] replace bedtools bamtofastq with samtools fastq (direct fastq.gz) --- modules/prokka.nf | 7 +------ modules/reads_deduplication.nf | 3 +-- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/modules/prokka.nf b/modules/prokka.nf index bb2c305..d2341c3 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -13,12 +13,7 @@ process PROKKA { """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk - - gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - then - rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - fi + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff """ } diff --git a/modules/reads_deduplication.nf b/modules/reads_deduplication.nf index 72b8ff3..c675efd 100644 --- a/modules/reads_deduplication.nf +++ b/modules/reads_deduplication.nf @@ -24,8 +24,7 @@ process READS_DEDUPLICATION { samtools idxstats ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.idxstats samtools flagstat ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.flagstat samtools sort -n -o ${sampleId}.filtered.sort.bam ${sampleId}.filtered.bam - bedtools bamtofastq -i ${sampleId}.filtered.sort.bam -fq ${sampleId}_R1_dedup.fastq -fq2 ${sampleId}_R2_dedup.fastq - gzip ${sampleId}_R1_dedup.fastq ; gzip ${sampleId}_R2_dedup.fastq + samtools fastq -N -1 ${sampleId}_R1_dedup.fastq.gz -2 ${sampleId}_R2_dedup.fastq.gz ${sampleId}.filtered.sort.bam rm ${sampleId}.sort.bam rm ${sampleId}.fixmate.bam rm ${sampleId}.fixmate.positionsort.bam -- GitLab From 0fa08f53c1383bb4d20bb5656169fee4711d8101 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 14:13:38 +0100 Subject: [PATCH 19/36] correct eggnog mapper version bug while not use --- bin/scrape_software_versions.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 86f979f..6b74a59 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -2,6 +2,7 @@ from __future__ import print_function from collections import OrderedDict import re +import os regexes = { 'metagWGS': ['v_pipeline.txt', r"(\S+)"], @@ -49,11 +50,12 @@ results['Eggnog-Mapper'] = '<span style="color:#999999;\">N/A</span>' # Search each file using its regex for k, v in regexes.items(): - with open(v[0]) as x: - versions = x.read() - match = re.search(v[1], versions) - if match: - results[k] = "v{}".format(match.group(1)) + if os.path.exists(v[0]): + with open(v[0]) as x: + versions = x.read() + match = re.search(v[1], versions) + if match: + results[k] = "v{}".format(match.group(1)) # Remove software set to false in results for k in results: -- GitLab From c95e3a73f2840b70e5c333b0eed9cf50cf9ac97a Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:54:20 +0100 Subject: [PATCH 20/36] correct host + taxonomy_dir paths --- functional_tests/expected_processes_HiFi.tsv | 4 +-- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index 4555d12..e278d4c 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 1f0ab4c..9d09ccf 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 -- GitLab From b8c84a53c78a6d50dd3ae3be962f8de2bcbddb50 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 21/36] update docs + add environement variables --- docs/usage.md | 8 +++--- functional_tests/README.md | 42 +++++++++++++++++++++--------- functional_tests/launch_example.sh | 2 +- 3 files changed, 35 insertions(+), 17 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 924523d..a476cfb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,9 +10,9 @@ > ``` > sample,fastq_1,fastq_2 - > a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz - > a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz - > c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz + > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz + > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz + > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz > ``` 4. Run a basic script: @@ -33,7 +33,7 @@ > nextflow run -profile test_genotoul_workq metagwgs/main.nf \ > --type 'SR' \ > --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \ - > --skip_host_filter --skip_kaiju + > --skip_host_filter --skip_kaiju --stop_at_clean > ``` > **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3. diff --git a/functional_tests/README.md b/functional_tests/README.md index 387ff1c..4d56af4 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -5,18 +5,17 @@ 1. Install metagwgs as described here: [installation doc](../docs/installation.md) 2. Get datasets: two datasets are currently available for these functional tests at `https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git` - Replace "\<dataset\>" with either "small" or "mag": ``` - git clone --branch <dataset> git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git + git clone git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git or - wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/archive/<dataset>/metagwgs-test-datasets-<dataset>.tar.gz + wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git ``` -3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-10-19.tar.gz) and decompress its contents in any folder. This archive contains data banks for: +3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz) and decompress its contents in any folder. This archive contains data banks for: - **Kaiju** (_kaijudb_refseq_2020-05-25_) - **Diamond** (_refseq_bacteria_2021-05-20_) - - **NCBI Taxonomy** (_taxonomy_2021-08-23_) + - **NCBI Taxonomy** (_taxonomy_2021-12-7_ ) - **Eggnog Mapper** (_eggnog-mapper-2.0.4-rf1_) @@ -30,15 +29,34 @@ To launch functional tests, you need to be located at the root of the folder whe - by providing the results folder of a pipeline already exectuted ``` cd test_folder -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results +export METAG_PATH="/path/to/sources" +export DATASET="/path/to/metagwgs-test-datasets" +python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results ``` - by providing a script which will launch the nextflow pipeline [see example](./launch_example.sh) (this example is designed for the "small" dataset with --min_contigs_cpm>1000, using slurm) -``` -mkdir test_folder -cd test_folder -cp <metagwgs-src>/functional_tests/launch_example.sh ./ -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results --script launch_example.sh -``` + + 1. create working directory + ``` + mkdir test_folder + cd test_folder + ``` + + 2.set enviroment variables and load module + + ``` + export METAG_PATH="/path/to/sources" + export DATASET="/path/to/metagwgs-test-datasets" + export DATABANK="/path/to/FT_banks_2021-10-19" + export EGGNOG_DB="$DATABANK/eggnog-mapper-2.0.4-rf1/data" + module load system/Python-3.7.4 + ``` + + 3.launch functional test + + ``` + cp $METAG_PATH/functional_tests/launch_example.sh ./ + python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results --script launch_example.sh + ``` >**NOTE: more information on the command used to produce each dataset in [small](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/small) and [mag](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/mag) READMEs** diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 3a95935..7d69bdd 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq main.nf --type 'SR' --input 'metagwgs-test-datasets/small/input/samplesheet.csv' --host_fasta 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir 'FT_banks_2021-10-19/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank 'FT_banks_2021-10-19/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir 'FT_banks_2021-10-19/eggnog-mapper-2.0.4-rf1/data' --taxonomy_dir 'FT_banks_2021-10-19/taxonomy_2021-08-23' --stop_at_clean -with-report -with-timeline -with-trace -with-dag" \ No newline at end of file + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 944d0efb99401970b3ce20bbeba4624f7660462c Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 10:44:00 +0100 Subject: [PATCH 22/36] remove diamond bank necessity when not use --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 46bccb4..9a05ad1 100644 --- a/main.nf +++ b/main.nf @@ -166,7 +166,7 @@ workflow { skip_clean = true } - if ( !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { + if ( !(params.stop_at_clean) && !(params.stop_at_assembly) && !(params.stop_at_filtering) && !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { exit 1, "You must specify --stop_at_structural_annot or specify a diamond bank with --diamond_bank" } header = getAndCheckHeader() -- GitLab From e6fd319d34a195744761b992089c8e27fa080daf Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 13:02:29 +0100 Subject: [PATCH 23/36] update functional_tests with new profiles --- functional_tests/README.md | 2 +- functional_tests/expected_processes_HiFi.tsv | 10 +++--- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- functional_tests/launch_example.sh | 2 +- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/functional_tests/README.md b/functional_tests/README.md index 4d56af4..25f1b36 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -150,7 +150,7 @@ To use it : ``` cut -f 1 $METAG_PATH/functional_tests/expected_processes_sr.tsv | tail -n +2 > $OUTDIR/cmd_sr.sh ``` - > the commands use profile `test_genotoul_workq` + > the commands use profile `test,genotoul` - replace path in the samplesheet : ``` sed -i -e "s,\$DATASET,$DATASET,g" $DATASET/small/input/samplesheet.csv diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index e278d4c..cf9eacf 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 9d09ccf..4f146c8 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 7d69bdd..0905b24 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 69c1bb09c0157c5a34fd35c3bdb1d5fe7aa05281 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 16:54:03 +0100 Subject: [PATCH 24/36] Check gff validity (issue : check point prokka) --- modules/prokka.nf | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/prokka.nf b/modules/prokka.nf index 44c3475..bb2c305 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -7,11 +7,18 @@ process PROKKA { output: tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results path "PROKKA_${sampleId}/${sampleId}.txt", emit: report + path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results script: """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk + + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + then + rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + fi """ } -- GitLab From c2523f7e15ba935177ec4eec7ab1cb9fe8c8fb1d Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Thu, 13 Jan 2022 09:46:12 +0100 Subject: [PATCH 25/36] replace bedtools bamtofastq with samtools fastq (direct fastq.gz) --- modules/prokka.nf | 7 +------ modules/reads_deduplication.nf | 3 +-- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/modules/prokka.nf b/modules/prokka.nf index bb2c305..d2341c3 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -13,12 +13,7 @@ process PROKKA { """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk - - gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - then - rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - fi + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff """ } diff --git a/modules/reads_deduplication.nf b/modules/reads_deduplication.nf index 72b8ff3..c675efd 100644 --- a/modules/reads_deduplication.nf +++ b/modules/reads_deduplication.nf @@ -24,8 +24,7 @@ process READS_DEDUPLICATION { samtools idxstats ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.idxstats samtools flagstat ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.flagstat samtools sort -n -o ${sampleId}.filtered.sort.bam ${sampleId}.filtered.bam - bedtools bamtofastq -i ${sampleId}.filtered.sort.bam -fq ${sampleId}_R1_dedup.fastq -fq2 ${sampleId}_R2_dedup.fastq - gzip ${sampleId}_R1_dedup.fastq ; gzip ${sampleId}_R2_dedup.fastq + samtools fastq -N -1 ${sampleId}_R1_dedup.fastq.gz -2 ${sampleId}_R2_dedup.fastq.gz ${sampleId}.filtered.sort.bam rm ${sampleId}.sort.bam rm ${sampleId}.fixmate.bam rm ${sampleId}.fixmate.positionsort.bam -- GitLab From 2b61f6742221afba3e61fd61026dcf1fba9459c4 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 14:13:38 +0100 Subject: [PATCH 26/36] correct eggnog mapper version bug while not use --- bin/scrape_software_versions.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 86f979f..6b74a59 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -2,6 +2,7 @@ from __future__ import print_function from collections import OrderedDict import re +import os regexes = { 'metagWGS': ['v_pipeline.txt', r"(\S+)"], @@ -49,11 +50,12 @@ results['Eggnog-Mapper'] = '<span style="color:#999999;\">N/A</span>' # Search each file using its regex for k, v in regexes.items(): - with open(v[0]) as x: - versions = x.read() - match = re.search(v[1], versions) - if match: - results[k] = "v{}".format(match.group(1)) + if os.path.exists(v[0]): + with open(v[0]) as x: + versions = x.read() + match = re.search(v[1], versions) + if match: + results[k] = "v{}".format(match.group(1)) # Remove software set to false in results for k in results: -- GitLab From 6b4dd74d90456253a3712d5540bcbf637d7e1552 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:54:20 +0100 Subject: [PATCH 27/36] correct host + taxonomy_dir paths --- functional_tests/expected_processes_HiFi.tsv | 4 +-- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index 4555d12..e278d4c 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 1f0ab4c..9d09ccf 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-08-23 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 -- GitLab From 29195043e4a67b39c830a67f69072ce27f19bbc4 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 28/36] update docs + add environement variables --- functional_tests/README.md | 42 +++++++++++++++++++++++++++----------- 1 file changed, 30 insertions(+), 12 deletions(-) diff --git a/functional_tests/README.md b/functional_tests/README.md index 5b4be13..4d56af4 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -5,18 +5,17 @@ 1. Install metagwgs as described here: [installation doc](../docs/installation.md) 2. Get datasets: two datasets are currently available for these functional tests at `https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git` - Replace "\<dataset\>" with either "small" or "mag": ``` - git clone --branch <dataset> git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git + git clone git@forgemia.inra.fr:genotoul-bioinfo/metagwgs-test-datasets.git or - wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/archive/<dataset>/metagwgs-test-datasets-<dataset>.tar.gz + wget https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets.git ``` -3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz ) and decompress its contents in any folder. This archive contains data banks for: +3. Get data banks: download [this archive](http://genoweb.toulouse.inra.fr/~choede/FT_banks_2021-12-16.tar.gz) and decompress its contents in any folder. This archive contains data banks for: - **Kaiju** (_kaijudb_refseq_2020-05-25_) - **Diamond** (_refseq_bacteria_2021-05-20_) - - **NCBI Taxonomy** (_taxonomy_2021-08-23_) + - **NCBI Taxonomy** (_taxonomy_2021-12-7_ ) - **Eggnog Mapper** (_eggnog-mapper-2.0.4-rf1_) @@ -30,15 +29,34 @@ To launch functional tests, you need to be located at the root of the folder whe - by providing the results folder of a pipeline already exectuted ``` cd test_folder -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results +export METAG_PATH="/path/to/sources" +export DATASET="/path/to/metagwgs-test-datasets" +python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results ``` - by providing a script which will launch the nextflow pipeline [see example](./launch_example.sh) (this example is designed for the "small" dataset with --min_contigs_cpm>1000, using slurm) -``` -mkdir test_folder -cd test_folder -cp <metagwgs-src>/functional_tests/launch_example.sh ./ -python <metagwgs-src>/functional_tests/main.py -step 07_taxo_affi -exp_dir metagwgs-test-datasets/small/output -obs_dir ./results --script launch_example.sh -``` + + 1. create working directory + ``` + mkdir test_folder + cd test_folder + ``` + + 2.set enviroment variables and load module + + ``` + export METAG_PATH="/path/to/sources" + export DATASET="/path/to/metagwgs-test-datasets" + export DATABANK="/path/to/FT_banks_2021-10-19" + export EGGNOG_DB="$DATABANK/eggnog-mapper-2.0.4-rf1/data" + module load system/Python-3.7.4 + ``` + + 3.launch functional test + + ``` + cp $METAG_PATH/functional_tests/launch_example.sh ./ + python $METAG_PATH/functional_tests/main.py -step 07_taxo_affi -exp_dir $DATASET/small/output -obs_dir ./results --script launch_example.sh + ``` >**NOTE: more information on the command used to produce each dataset in [small](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/small) and [mag](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets/-/tree/mag) READMEs** -- GitLab From 96471aed1daaea4386c362e216f47057188df38e Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 10:44:00 +0100 Subject: [PATCH 29/36] remove diamond bank necessity when not use --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index de00ac8..67a944c 100644 --- a/main.nf +++ b/main.nf @@ -165,7 +165,7 @@ workflow { skip_clean = true } - if ( !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { + if ( !(params.stop_at_clean) && !(params.stop_at_assembly) && !(params.stop_at_filtering) && !(params.stop_at_structural_annot) && !(params.diamond_bank) ) { exit 1, "You must specify --stop_at_structural_annot or specify a diamond bank with --diamond_bank" } header = getAndCheckHeader() -- GitLab From 828d606bf45a4fdc4fcf5500badd95e1de633adb Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 30/36] update docs + add environement variables --- docs/usage.md | 8 ++++---- functional_tests/launch_example.sh | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 1a1c665..def331d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -10,9 +10,9 @@ > ``` > sample,fastq_1,fastq_2 - > a1,$DASTASET/a1_R1.fastq.gz,$DASTASET/a1_R2.fastq.gz - > a2,$DASTASET/a2_R1.fastq.gz,$DASTASET/a2_R2.fastq.gz - > c,$DASTASET/c_R1.fastq.gz,$DASTASET/c_R2.fastq.gz + > a1,$DATASET/a1_R1.fastq.gz,$DATASET/a1_R2.fastq.gz + > a2,$DATASET/a2_R1.fastq.gz,$DATASET/a2_R2.fastq.gz + > c,$DATASET/c_R1.fastq.gz,$DATASET/c_R2.fastq.gz > ``` 4. Run a basic script: @@ -33,7 +33,7 @@ > nextflow run -profile test_genotoul_workq metagwgs/main.nf \ > --type 'SR' \ > --input 'metagwgs-test-datasets/small/input/samplesheet.csv' \ - > --skip_host_filter --skip_kaiju + > --skip_host_filter --skip_kaiju --stop_at_clean > ``` > **NOTE:** you can change Nextflow and Singularity versions with other versions available on the cluster (see all versions with `search_module ToolName`). Nextflow version must be >= v20 and Singularity version must be >= v3. diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 3a95935..7d69bdd 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq main.nf --type 'SR' --input 'metagwgs-test-datasets/small/input/samplesheet.csv' --host_fasta 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index 'metagwgs-test-datasets/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir 'FT_banks_2021-10-19/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank 'FT_banks_2021-10-19/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir 'FT_banks_2021-10-19/eggnog-mapper-2.0.4-rf1/data' --taxonomy_dir 'FT_banks_2021-10-19/taxonomy_2021-08-23' --stop_at_clean -with-report -with-timeline -with-trace -with-dag" \ No newline at end of file + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 43329377357dbb06d8a1bad0afc6d4b303d945a6 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 13:02:29 +0100 Subject: [PATCH 31/36] update functional_tests with new profiles --- functional_tests/README.md | 2 +- functional_tests/expected_processes_HiFi.tsv | 10 +++--- functional_tests/expected_processes_sr.tsv | 34 ++++++++++---------- functional_tests/launch_example.sh | 2 +- 4 files changed, 24 insertions(+), 24 deletions(-) diff --git a/functional_tests/README.md b/functional_tests/README.md index 4d56af4..25f1b36 100644 --- a/functional_tests/README.md +++ b/functional_tests/README.md @@ -150,7 +150,7 @@ To use it : ``` cut -f 1 $METAG_PATH/functional_tests/expected_processes_sr.tsv | tail -n +2 > $OUTDIR/cmd_sr.sh ``` - > the commands use profile `test_genotoul_workq` + > the commands use profile `test,genotoul` - replace path in the samplesheet : ``` sed -i -e "s,\$DATASET,$DATASET,g" $DATASET/small/input/samplesheet.csv diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index e278d4c..cf9eacf 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 9d09ccf..4f146c8 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 7d69bdd..0905b24 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -- GitLab From 04ddeaa0d0a0b5356172e19f8f92db3256577dea Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 16:54:03 +0100 Subject: [PATCH 32/36] Check gff validity (issue : check point prokka) --- modules/prokka.nf | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/modules/prokka.nf b/modules/prokka.nf index 44c3475..bb2c305 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -7,11 +7,18 @@ process PROKKA { output: tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results path "PROKKA_${sampleId}/${sampleId}.txt", emit: report + path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results script: """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk + + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + then + rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt + fi """ } -- GitLab From 66af6629c459db2e19362387a978902323309aa2 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Thu, 13 Jan 2022 09:46:12 +0100 Subject: [PATCH 33/36] replace bedtools bamtofastq with samtools fastq (direct fastq.gz) --- modules/prokka.nf | 7 +------ modules/reads_deduplication.nf | 3 +-- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/modules/prokka.nf b/modules/prokka.nf index bb2c305..d2341c3 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -13,12 +13,7 @@ process PROKKA { """ prokka --metagenome --noanno --rawproduct --outdir PROKKA_${sampleId} --prefix ${sampleId} ${assembly_file} --centre X --compliant --cpus ${task.cpus} rm PROKKA_${sampleId}/*.gbk - - gt gff3validator PROKKA_${sampleId}/${sampleId}.gff > PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - if grep -Fxqv "input is valid GFF3" PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - then - rm PROKKA_${sampleId}/${sampleId}_gff3_validator.txt - fi + gt gff3validator PROKKA_${sampleId}/${sampleId}.gff """ } diff --git a/modules/reads_deduplication.nf b/modules/reads_deduplication.nf index 72b8ff3..c675efd 100644 --- a/modules/reads_deduplication.nf +++ b/modules/reads_deduplication.nf @@ -24,8 +24,7 @@ process READS_DEDUPLICATION { samtools idxstats ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.idxstats samtools flagstat ${sampleId}.filtered.bam > ${sampleId}.count_reads_on_contigs.flagstat samtools sort -n -o ${sampleId}.filtered.sort.bam ${sampleId}.filtered.bam - bedtools bamtofastq -i ${sampleId}.filtered.sort.bam -fq ${sampleId}_R1_dedup.fastq -fq2 ${sampleId}_R2_dedup.fastq - gzip ${sampleId}_R1_dedup.fastq ; gzip ${sampleId}_R2_dedup.fastq + samtools fastq -N -1 ${sampleId}_R1_dedup.fastq.gz -2 ${sampleId}_R2_dedup.fastq.gz ${sampleId}.filtered.sort.bam rm ${sampleId}.sort.bam rm ${sampleId}.fixmate.bam rm ${sampleId}.fixmate.positionsort.bam -- GitLab From 20dc1171f1236472c1d6206f8268b4abf5a632ca Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Mon, 10 Jan 2022 15:55:47 +0100 Subject: [PATCH 34/36] update docs + add environement variables --- functional_tests/launch_example.sh | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index 0905b24..baef67d 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,4 +1,8 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ +<<<<<<< HEAD --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" +======= + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" +>>>>>>> update docs + add environement variables -- GitLab From ee4c12a05ee96642f5203fe8bc181a693bb6b7c6 Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Tue, 11 Jan 2022 13:02:29 +0100 Subject: [PATCH 35/36] update functional_tests with new profiles --- functional_tests/launch_example.sh | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index baef67d..3750a6d 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,8 +1,5 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ -<<<<<<< HEAD - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" -======= - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" ->>>>>>> update docs + add environement variables + + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" \ No newline at end of file -- GitLab From a689edb8c4ac21e991bc2abbbd4f18d494ef87ea Mon Sep 17 00:00:00 2001 From: Maina Vienne <maina.vienne@inrae.fr> Date: Fri, 14 Jan 2022 09:30:56 +0100 Subject: [PATCH 36/36] update functional test to take into account new taxonomy parameters --- functional_tests/expected_processes_HiFi.tsv | 4 +-- functional_tests/expected_processes_sr.tsv | 32 ++++++++++---------- functional_tests/launch_example.sh | 3 +- modules/prokka.nf | 1 - 4 files changed, 19 insertions(+), 21 deletions(-) diff --git a/functional_tests/expected_processes_HiFi.tsv b/functional_tests/expected_processes_HiFi.tsv index cf9eacf..ca9dbbd 100644 --- a/functional_tests/expected_processes_HiFi.tsv +++ b/functional_tests/expected_processes_HiFi.tsv @@ -1,6 +1,6 @@ cmd outputdir DATABASES:INDEX_KAIJU DATABASES:DOWNLOAD_TAXONOMY_DB DATABASES:EGGNOG_MAPPER_DB SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:MINIMAP2 SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS -mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/hifi_all ; cd $OUTDIR/hifi_all ;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump $OUTDIR/hifi_all 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 mkdir $OUTDIR/hifi_stop_at_structural_annot;cd $OUTDIR/hifi_stop_at_structural_annot; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --stop_at_structural_annot $OUTDIR/hifi_stop_at_structural_annot 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 mkdir $OUTDIR/skip_func_annot-skip_taxo_affi; cd $OUTDIR/skip_func_annot-skip_taxo_affi;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot;cp ../nextflow.config .; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --eggnog_mapper_db_dir `echo $EGGNOG_DB` --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump –skip_func_annot $OUTDIR/skip_func_annot 0 0 0 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 mkdir $OUTDIR/skip_taxo_affi; cd $OUTDIR/skip_taxo_affi;nextflow run -profile test,genotoul $METAG_PATH/main.nf --type HIFI --input `echo $DATASET`/hifi/input/samplesheet.csv --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --skip_taxo_affi $OUTDIR/skip_taxo_affi 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/expected_processes_sr.tsv b/functional_tests/expected_processes_sr.tsv index 4f146c8..26f8a39 100644 --- a/functional_tests/expected_processes_sr.tsv +++ b/functional_tests/expected_processes_sr.tsv @@ -1,22 +1,22 @@ cmd outputdir SR:S01_CLEAN_QC:FASTQC_RAW SR:S01_CLEAN_QC:CUTADAPT SR:S01_CLEAN_QC:SICKLE SR:S01_CLEAN_QC:HOST_FILTER SR:S01_CLEAN_QC:FASTQC_CLEANED SR:S01_CLEAN_QC:KAIJU_AND_MERGE:KAIJU SR:S01_CLEAN_QC:KAIJU_AND_MERGE:MERGE_KAIJU SR:S02_ASSEMBLY:ASSEMBLY SR:S02_ASSEMBLY:ASSEMBLY_QUAST SR:S02_ASSEMBLY:READS_DEDUPLICATION SR:S03_FILTERING:CHUNK_ASSEMBLY_FILTER SR:S03_FILTERING:MERGE_ASSEMBLY_FILTER SH:S04_STRUCTURAL_ANNOT:PROKKA SH:S04_FILTERED_QUAST SH:S04_STRUCTURAL_ANNOT:RENAME_CONTIGS_AND_GENES SH:S05_ALIGNMENT:DIAMOND SH:S05_ALIGNMENT:BWA_MEM SH:S06_FUNC_ANNOT:CD_HIT:INDIVIDUAL_CD_HIT SH:S06_FUNC_ANNOT:EGGNOG_MAPPER SH:S06_FUNC_ANNOT:BEST_HITS SH:S06_FUNC_ANNOT:QUANTIFICATION:FEATURE_COUNTS SH:S06_FUNC_ANNOT:CD_HIT:GLOBAL_CD_HIT SH:S06_FUNC_ANNOT:QUANTIFICATION:QUANTIFICATION_TABLE SH:S06_FUNC_ANNOT:MERGE_QUANT_ANNOT_BEST SH:S06_FUNC_ANNOT:FUNCTIONAL_ANNOT_TABLE SH:S07_TAXO_AFFI:ASSIGN_TAXONOMY SH:S07_TAXO_AFFI:QUANTIF_AND_TAXONOMIC_TABLE_CONTIGS mkdir $OUTDIR/stop_at_clean ; cd $OUTDIR/stop_at_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 -with-report -with-timeline -with-trace --stop_at_clean $OUTDIR/stop_at_clean 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter --skip_kaiju $OUTDIR/skip_sickle-skip_host_filter-skip_kaiju 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_host_filter ; cd $OUTDIR/skip_sickle-skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_host_filter $OUTDIR/skip_sickle-skip_host_filter 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle-skip_kaiju ; cd $OUTDIR/skip_sickle-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle --skip_kaiju $OUTDIR/skip_sickle-skip_kaiju 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_sickle ; cd $OUTDIR/skip_sickle ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_sickle $OUTDIR/skip_sickle 1 1 0 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter-skip_kaiju ; cd $OUTDIR/skip_host_filter-skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter --skip_kaiju $OUTDIR/skip_host_filter-skip_kaiju 1 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_host_filter ; cd $OUTDIR/skip_host_filter ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_host_filter $OUTDIR/skip_host_filter 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_kaiju ; cd $OUTDIR/skip_kaiju ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_clean --skip_kaiju $OUTDIR/skip_kaiju 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_assembly ; cd $OUTDIR/stop_at_assembly ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_assembly $OUTDIR/stop_at_assembly 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_clean ; cd $OUTDIR/skip_clean ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_assembly --skip_clean $OUTDIR/skip_clean 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_filtering ; cd $OUTDIR/stop_at_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_filtering $OUTDIR/stop_at_filtering 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/stop_at_structural_annot ; cd $OUTDIR/stop_at_structural_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_structural_annot $OUTDIR/stop_at_structural_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_filtering ; cd $OUTDIR/skip_filtering ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --stop_at_structural_annot --skip_filtering $OUTDIR/skip_filtering 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 -mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 -mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 -mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --taxonomy_dir `echo $DATABANK`/taxonomy_2021-12-7 -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 +mkdir $OUTDIR/all ; cd $OUTDIR/all ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace $OUTDIR/all 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +mkdir $OUTDIR/skip_func_annot-skip_taxo_affi ; cd $OUTDIR/skip_func_annot-skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --skip_func_annot --skip_taxo_affi $OUTDIR/skip_func_annot-skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 +mkdir $OUTDIR/skip_func_annot ; cd $OUTDIR/skip_func_annot ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --skip_func_annot $OUTDIR/skip_func_annot 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 1 1 +mkdir $OUTDIR/skip_taxo_affi ; cd $OUTDIR/skip_taxo_affi ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input `echo $DATASET`/small/input/samplesheet.csv --host_fasta `echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa --host_index "`echo $DATASET`/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}" --kaiju_db_dir `echo $DATABANK`/kaijudb_refseq_2020-05-25 --diamond_bank `echo $DATABANK`/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd --eggnog_mapper_db_dir `echo $EGGNOG_DB` --accession2taxid `echo $DATABANK`/taxonomy_2021-12-7/prot.accession2taxid.FULL --taxdump `echo $DATABANK`/taxonomy_2021-12-7/new_taxdump -with-report -with-timeline -with-trace --skip_taxo_affi $OUTDIR/skip_taxo_affi 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 diff --git a/functional_tests/launch_example.sh b/functional_tests/launch_example.sh index ecacf0d..0bbc87d 100644 --- a/functional_tests/launch_example.sh +++ b/functional_tests/launch_example.sh @@ -1,5 +1,4 @@ #!/bin/bash sbatch -W -p workq -J functional_test --mem=6G \ - - --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --taxonomy_dir '$DATABANK/taxonomy_2021-12-7' -with-report -with-timeline -with-trace -with-dag" + --wrap="module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test,genotoul $METAG_PATH/main.nf --type 'SR' --input '$DATASET/small/input/samplesheet.csv' --host_fasta '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa' --host_index '$DATASET/small/input/host/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '$DATABANK/kaijudb_refseq_2020-05-25' --min_contigs_cpm 1000 --diamond_bank '$DATABANK/refseq_bacteria_2021-05-20/refseq_bacteria_100000.dmnd' --eggnog_mapper_db_dir '$EGGNOG_DB' --accession2taxid '$DATABANK/taxonomy_2021-12-7/prot.accession2taxid.FULL' --taxdump '$DATABANK/taxonomy_2021-12-7/new_taxdump' -with-report -with-timeline -with-trace -with-dag" diff --git a/modules/prokka.nf b/modules/prokka.nf index d2341c3..984e972 100644 --- a/modules/prokka.nf +++ b/modules/prokka.nf @@ -7,7 +7,6 @@ process PROKKA { output: tuple val(sampleId), path("PROKKA_${sampleId}"), emit: prokka_results path "PROKKA_${sampleId}/${sampleId}.txt", emit: report - path "PROKKA_${sampleId}/${sampleId}_gff3_validator.txt",emit: gff3_validator_results script: """ -- GitLab