From 1d54341fcf4a305e13d906868df993d44c95a0d1 Mon Sep 17 00:00:00 2001
From: nservant <nicolas.servant@curie.fr>
Date: Fri, 16 Apr 2021 20:15:22 +0200
Subject: [PATCH] [MODIF] issue with stats file
---
main.nf | 44 ++++++++++++++++++++++++++------------------
1 file changed, 26 insertions(+), 18 deletions(-)
diff --git a/main.nf b/main.nf
index c035bb9..dc0ebe1 100644
--- a/main.nf
+++ b/main.nf
@@ -682,15 +682,15 @@ else{
process remove_duplicates {
tag "$sample"
label 'process_highmem'
- publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode
-
+ publishDir "${params.outdir}/hicpro/valid_pairs", mode: params.publish_dir_mode,
+ saveAs: {filename -> filename.endsWith("stat") ? "stats/$filename" : "$filename"}
input:
set val(sample), file(vpairs) from valid_pairs.groupTuple()
output:
set val(sample), file("*.allValidPairs") into ch_vpairs, ch_vpairs_cool
file("stats/") into mqc_mergestat
- file("stats/*/*") into all_mergestat
+ file("*mergestat") into all_mergestat
script:
if ( ! params.keep_dups ){
@@ -701,26 +701,32 @@ process remove_duplicates {
sort -S 50% -k2,2V -k3,3n -k5,5V -k6,6n -m ${vpairs} | \
awk -F"\\t" 'BEGIN{c1=0;c2=0;s1=0;s2=0}(c1!=\$2 || c2!=\$5 || s1!=\$3 || s2!=\$6){print;c1=\$2;c2=\$5;s1=\$3;s2=\$6}' > ${sample}.allValidPairs
- echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
- cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
- echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
- cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
+ echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat
+ cat ${vpairs} | wc -l >> ${sample}_allValidPairs.mergestat
+ echo -n "valid_interaction_rmdup\t" >> ${sample}_allValidPairs.mergestat
+ cat ${sample}.allValidPairs | wc -l >> ${sample}_allValidPairs.mergestat
## Count short range (<20000) vs long range contacts
- awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
-
+ awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> ${sample}_allValidPairs.mergestat
+
+ ## For MultiQC
+ mkdir -p stats/${sample}
+ cp ${sample}_allValidPairs.mergestat stats/${sample}/
"""
}else{
"""
- mkdir -p stats/${sample}
cat ${vpairs} > ${sample}.allValidPairs
- echo -n "valid_interaction\t" > stats/${sample}/${sample}_allValidPairs.mergestat
- cat ${vpairs} | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
- echo -n "valid_interaction_rmdup\t" >> stats/${sample}/${sample}_allValidPairs.mergestat
- cat ${sample}.allValidPairs | wc -l >> stats/${sample}/${sample}_allValidPairs.mergestat
+ echo -n "valid_interaction\t" > ${sample}_allValidPairs.mergestat
+ cat ${vpairs} | wc -l >> ${sample}_allValidPairs.mergestat
+ echo -n "valid_interaction_rmdup\t" >> ${sample}_allValidPairs.mergestat
+ cat ${sample}.allValidPairs | wc -l >> ${sample}_allValidPairs.mergestat
## Count short range (<20000) vs long range contacts
- awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> stats/${sample}/${sample}_allValidPairs.mergestat
+ awk 'BEGIN{cis=0;trans=0;sr=0;lr=0} \$2 == \$5{cis=cis+1; d=\$6>\$3?\$6-\$3:\$3-\$6; if (d<=20000){sr=sr+1}else{lr=lr+1}} \$2!=\$5{trans=trans+1}END{print "trans_interaction\\t"trans"\\ncis_interaction\\t"cis"\\ncis_shortRange\\t"sr"\\ncis_longRange\\t"lr}' ${sample}.allValidPairs >> ${sample}_allValidPairs.mergestat
+
+ ## For MultiQC
+ mkdir -p stats/${sample}
+ cp ${sample}_allValidPairs.mergestat stats/${sample}/
"""
}
}
@@ -728,14 +734,15 @@ process remove_duplicates {
process merge_stats {
tag "$ext"
label 'process_low'
- publishDir "${params.outdir}/hicpro/", mode: params.publish_dir_mode
+ publishDir "${params.outdir}/hicpro/", mode: params.publish_dir_mode,
+ saveAs: {filename -> filename.endsWith("stat") ? "stats/$filename" : "$filename"}
input:
set val(prefix), file(fstat) from all_mapstat.groupTuple().concat(all_pairstat.groupTuple(), all_rsstat.groupTuple())
output:
file("stats/") into mqc_mstats
- file("stats/*/*") into all_mstats
+ file("*stat") into all_mstats
script:
sample = prefix.toString() - ~/(_R1|_R2|_val_1|_val_2|_1|_2)/
@@ -743,8 +750,9 @@ process merge_stats {
if ( (fstat =~ /.pairstat/) ){ ext = "mpairstat" }
if ( (fstat =~ /.RSstat/) ){ ext = "mRSstat" }
"""
+ merge_statfiles.py -f ${fstat} > ${prefix}.${ext}
mkdir -p stats/${sample}
- merge_statfiles.py -f ${fstat} > stats/${sample}/${prefix}.${ext}
+ cp ${prefix}.${ext} stats/${sample}/
"""
}
--
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