nf-core_modules/modules/cnvpytor/histogram/main.nf

43 lines
1.2 KiB
Text
Raw Normal View History

process CNVPYTOR_HISTOGRAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
2022-03-31 08:53:26 +00:00
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
input:
tuple val(meta), path(pytor)
output:
tuple val(meta), path("${pytor.baseName}.pytor") , emit: pytor
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: '1000'
"""
cnvpytor \\
-root $pytor \\
-his $args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
stub:
"""
2022-04-04 11:18:02 +00:00
touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
}