From 309f80d7bbff74aa3439908222c47d2fbae431ff Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Mar 2021 17:24:26 +0100
Subject: [PATCH] samtools: add process to rename files for multiqc
---
src/nf_modules/samtools/main.nf | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 9599ec63..0ccc1dfe 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -200,3 +200,29 @@ process stats_bam {
samtools flagstat -@ ${task.cpus} -O tsv ${bam} > ${bam.simpleName}_stats.tsv
"""
}
+
+process flagstat_2_multiqc {
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(tsv), emit: tsv
+
+ output:
+ tuple val(file_id), path("*.txt"), emit: report
+"""
+mv ${tsv} ${tsv.simpleName}.flagstat.txt
+"""
+}
+
+process idxstat_2_multiqc {
+ tag "$file_id"
+
+ input:
+ tuple val(file_id), path(tsv), emit: tsv
+
+ output:
+ tuple val(file_id), path("*.txt"), emit: report
+"""
+mv ${tsv} ${tsv.simpleName}.idxstats.txt
+"""
+}
\ No newline at end of file
--
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