From ebb5cb65b97231bd3275331c793b562cd81fb816 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 29 Jan 2021 11:17:49 +0100
Subject: [PATCH] samtools: fix flagstats cmd
---
src/nf_modules/samtools/main.nf | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 0c04674d..3b0c8f34 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -90,7 +90,6 @@ process split_bam {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "$file_id"
- cpus = 2
input:
tuple val(file_id), path(bam)
@@ -100,8 +99,10 @@ process split_bam {
tuple val(file_id), path("*_reverse.bam*"), emit: bam_reverse
script:
"""
-samtools view -hb -F 0x10 ${bam} > ${file_id}_forward.bam &
-samtools view -hb -f 0x10 ${bam} > ${file_id}_reverse.bam
+samtools view --@ ${Math.round(task.cpus/2)} \
+ -hb -F 0x10 ${bam} > ${file_id}_forward.bam &
+samtools view --@ ${Math.round(task.cpus/2)} \
+ -hb -f 0x10 ${bam} > ${file_id}_reverse.bam
"""
}
@@ -124,9 +125,9 @@ samtools merge ${first_bam} ${second_bam} ${first_bam_id}_${second_file_id}.bam
"""
}
-process bam_stats {
+process stats_bam {
container = "${container_url}"
- label "big_mem_mono_cpus"
+ label "big_mem_multi_cpus"
tag "$file_id"
cpus = 2
@@ -137,6 +138,6 @@ process bam_stats {
tuple val(file_id), path("*.tsv"), emit: tsv
script:
"""
-samtools flagstat -O tsv ${bam} > ${file_id}.tsv
+samtools flagstat -@ ${task.cpus} -O tsv ${bam} > ${file_id}.tsv
"""
}
--
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