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fix samtools stats thread usage (#1975)

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* fix samtools stats thread usage

* fix checksums
This commit is contained in:
Matthias De Smet 2022-08-29 12:05:47 +02:00 committed by GitHub
parent baa2845d28
commit f4eab79459
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 6 additions and 6 deletions
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4
modules/samtools/stats/main.nf
View file

@ -1,6 +1,6 @@
process SAMTOOLS_STATS { process SAMTOOLS_STATS {
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 ?
@ -25,7 +25,7 @@ process SAMTOOLS_STATS {
""" """
samtools \\ samtools \\
stats \\ stats \\
--threads ${task.cpus-1} \\ --threads ${task.cpus} \\
${reference} \\ ${reference} \\
${input} \\ ${input} \\
> ${prefix}.stats > ${prefix}.stats

8
tests/modules/samtools/stats/test.yml
View file

@ -1,17 +1,17 @@
- name: samtools stats test_samtools_stats - name: samtools stats test_samtools_stats
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
tags: tags:
- samtools
- samtools/stats - samtools/stats
- samtools
files: files:
- path: output/samtools/test.stats - path: output/samtools/test.stats
md5sum: c1e9ad551281b0bca32be1c832d125af md5sum: 5e6fa3805f6d6b330262456746709239
- name: samtools stats test_samtools_stats_cram - name: samtools stats test_samtools_stats_cram
command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config command: nextflow run ./tests/modules/samtools/stats -entry test_samtools_stats_cram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/stats/nextflow.config
tags: tags:
- samtools
- samtools/stats - samtools/stats
- samtools
files: files:
- path: output/samtools/test.stats - path: output/samtools/test.stats
md5sum: 103cd7b19743c42dab9ce570144c6f36 md5sum: 916a8e5bfd97a53f806e5a14565631bb