From bbb99cb8d679555cc01c98766de7869f83283545 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Mon, 29 Aug 2022 13:11:58 +0200 Subject: [PATCH] Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads --- modules/samtools/flagstat/main.nf | 4 ++-- tests/modules/samtools/flagstat/test.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf index 03ec2dcf..c3152aca 100644 --- a/modules/samtools/flagstat/main.nf +++ b/modules/samtools/flagstat/main.nf @@ -1,6 +1,6 @@ process SAMTOOLS_FLAGSTAT { tag "$meta.id" - label 'process_low' + label 'process_single' conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? @@ -23,7 +23,7 @@ process SAMTOOLS_FLAGSTAT { """ samtools \\ flagstat \\ - --threads ${task.cpus-1} \\ + --threads ${task.cpus} \\ $bam \\ > ${prefix}.flagstat diff --git a/tests/modules/samtools/flagstat/test.yml b/tests/modules/samtools/flagstat/test.yml index 31762434..4351a2b7 100644 --- a/tests/modules/samtools/flagstat/test.yml +++ b/tests/modules/samtools/flagstat/test.yml @@ -1,8 +1,8 @@ - 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 tags: - - samtools - samtools/flagstat + - samtools files: - path: output/samtools/test.flagstat md5sum: 4f7ffd1e6a5e85524d443209ac97d783