nf-core_modules/modules/sexdeterrmine/main.nf
James A. Fellows Yates 90aef30f43
Set process label to process_single for modules with no task.cpus usage (#2076)
* Set process label to `process_single` for modules with no `task.cpus` usage

* Fix tests of 'borked' modules

* prettier

* More modules are single-threaded and can use process_single

* Adding process_single to hmmer/esl* modules

* Fix failing tests

* Prettier

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-09-19 11:54:47 +02:00

40 lines
1.2 KiB
Text

process SEXDETERRMINE {
tag "$meta.id"
label 'process_single'
conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
input:
tuple val(meta), path(depth)
path sample_list_file
output:
tuple val(meta), path("*.json"), emit: json
tuple val(meta), path("*.tsv") , emit: tsv
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
"""
sexdeterrmine \\
-I $depth \\
$sample_list \\
$args \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
END_VERSIONS
"""
}