From 24cb56374693a8fd6605e5a8f5585581ff0cd577 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Noirot=20C=C3=A9line?= <celine.noirot@inra.fr>
Date: Thu, 18 Aug 2022 09:29:27 +0200
Subject: [PATCH] Do checkpoint on values after Cdhit #30
---
modules/cd_hit.nf | 41 ++++++++++++++++++++++++++++++++++++-----
1 file changed, 36 insertions(+), 5 deletions(-)
diff --git a/modules/cd_hit.nf b/modules/cd_hit.nf
index af6913c..d1e7252 100644
--- a/modules/cd_hit.nf
+++ b/modules/cd_hit.nf
@@ -30,7 +30,7 @@ process GLOBAL_CD_HIT {
val pct_id
output:
- path "All-cd-hit-est.${pct_id}.fasta"
+ path "All-cd-hit-est.${pct_id}.fasta", emit: fasta_clusters
path "table_clstr.txt", emit: clstr_table
@@ -44,6 +44,38 @@ process GLOBAL_CD_HIT {
}
+// Global clustering with CD-HIT.
+process CHECK_METRICS {
+ label 'CD_HIT'
+
+ input:
+ path ech_fastas
+ path table_clstr
+ path fasta_cluster
+
+ script:
+ """
+ cat ${ech_fastas} | grep -c ">" > nb_inputed_seq_in_fasta.txt
+ grep -c ">" All-cd-hit-est.0.95.fasta > nb_clusters_in_fasta.txt
+ cut -f1 table_clstr.txt | sort -u | wc -l > nb_clusters.txt
+ cat table_clstr.txt | wc -l > nb_seq_clustered.txt
+
+ DIFF=\$(diff nb_clusters.txt nb_clusters_in_fasta.txt)
+ if [ "\$DIFF" != "" ]
+ then
+ echo "Error: nb cluster after cdhit (individual + global) not consistant [table VS fasta]"
+ exit 1
+ fi
+
+ DIFF=\$(diff nb_seq_clustered.txt nb_inputed_seq_in_fasta.txt)
+ if [ "\$DIFF" != "" ]
+ then
+ echo "Error: nb contigs after cdhit (individual + global) not consistant [table VS fasta]"
+ exit 1
+ fi
+ """
+
+}
workflow CD_HIT {
@@ -53,14 +85,13 @@ ch_percentage_identity // channel: val
main:
INDIVIDUAL_CD_HIT( ch_assembly, ch_percentage_identity )
-
ch_individual_clusters = INDIVIDUAL_CD_HIT.out.clstr_fasta.collect()
-
GLOBAL_CD_HIT(ch_individual_clusters , ch_percentage_identity )
+ ch_ffn = ch_assembly.flatMap{it -> it[1]}.collect()
+ CHECK_METRICS(ch_ffn, GLOBAL_CD_HIT.out.clstr_table , GLOBAL_CD_HIT.out.fasta_clusters)
emit:
individual_clstr_table = INDIVIDUAL_CD_HIT.out.clstr_table
global_clstr_table = GLOBAL_CD_HIT.out.clstr_table
-}
-
+}
\ No newline at end of file
--
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