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Fix/samtools flagstat (#1979)

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* fix samtools stats thread usage

* flagstat: fix threads
This commit is contained in:
Matthias De Smet 2022-08-29 13:11:58 +02:00 committed by GitHub
parent f4eab79459
commit bbb99cb8d6
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2 changed files with 3 additions and 3 deletions
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4
modules/samtools/flagstat/main.nf
View file

@ -1,6 +1,6 @@
process SAMTOOLS_FLAGSTAT { process SAMTOOLS_FLAGSTAT {
tag "$meta.id" tag "$meta.id"
label 'process_low' label 'process_single'
conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@ -23,7 +23,7 @@ process SAMTOOLS_FLAGSTAT {
""" """
samtools \\ samtools \\
flagstat \\ flagstat \\
--threads ${task.cpus-1} \\ --threads ${task.cpus} \\
$bam \\ $bam \\
> ${prefix}.flagstat > ${prefix}.flagstat

2
tests/modules/samtools/flagstat/test.yml
View file

@ -1,8 +1,8 @@
- name: samtools flagstat test_samtools_flagstat - name: samtools flagstat test_samtools_flagstat
command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/samtools/flagstat/nextflow.config command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config -c ./tests/modules/samtools/flagstat/nextflow.config
tags: tags:
- samtools
- samtools/flagstat - samtools/flagstat
- samtools
files: files:
- path: output/samtools/test.flagstat - path: output/samtools/test.flagstat
md5sum: 4f7ffd1e6a5e85524d443209ac97d783 md5sum: 4f7ffd1e6a5e85524d443209ac97d783