view 0.5.0/modules/samplesheet_check/main.nf @ 1:365849f031fd

"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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process SAMPLESHEET_CHECK {
    tag "$samplesheet"
    label "process_femto"

    module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
    conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
        'quay.io/biocontainers/python:3.9--1' }"

    input:
        path samplesheet

    output:
        path '*.csv'       , emit: csv
        path "versions.yml", emit: versions

    when:
        task.ext.when == null || task.ext.when

    script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/
        """
        check_samplesheet.py \\
            $samplesheet \\
            samplesheet.valid.csv

        cat <<-END_VERSIONS > versions.yml
        "${task.process}":
            python: \$( python --version | sed 's/Python //g' )
        END_VERSIONS
        """
}