From e9175cbdb66415563b541d34332db52801aa6dfa Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 2 Nov 2021 12:11:05 +0100
Subject: [PATCH] samtools and picardtools: add compatibility with mutliqc
---
src/nf_modules/picard/main.nf | 4 ++--
src/nf_modules/samtools/main.nf | 2 ++
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/src/nf_modules/picard/main.nf b/src/nf_modules/picard/main.nf
index 0d385805..449d5fd0 100644
--- a/src/nf_modules/picard/main.nf
+++ b/src/nf_modules/picard/main.nf
@@ -15,7 +15,7 @@ process mark_duplicate {
tuple val(file_id), path(bam)
output:
tuple val(file_id) , path("*.bam"), emit: bam
- path "*_report.txt", emit: report
+ path "*_report.dupinfo.txt", emit: report
script:
@@ -24,7 +24,7 @@ PicardCommandLine MarkDuplicates \
${params.mark_duplicate} \
INPUT=${bam} \
OUTPUT=${bam.baseName}_dedup.bam \
- METRICS_FILE=${bam.baseName}_picard_dedup_report.txt &> \
+ METRICS_FILE=${bam.baseName}_picard_dedup_report.dupinfo.txt &> \
picard_${bam.baseName}.log
"""
}
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index b9dcb72d..10df2042 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -270,9 +270,11 @@ process stats_bam {
output:
tuple val(file_id), path("*.tsv"), emit: tsv
+ tuple val(file_id), path("*.flagstat.txt"), emit: report
script:
"""
samtools flagstat -@ ${task.cpus} ${params.stats_bam} -O tsv ${bam} > ${bam.simpleName}.flagstat.txt
+cp ${bam.simpleName}.flagstat.txt ${bam.simpleName}.tsv
"""
}
--
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