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0
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1 process GEN_SAMPLESHEET {
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2 tag "${inputdir.simpleName}"
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3 label "process_pico"
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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6 conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/python:3.9--1' :
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9 'quay.io/biocontainers/python:3.9--1' }"
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10
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11 input:
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12 val inputdir
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13
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14 output:
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15 path '*.csv' , emit: csv
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16 path 'versions.yml', emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 // This script (fastq_dir_to_samplesheet.py) is distributed
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22 // as part of the pipeline nf-core/rnaseq/bin/. MIT License.
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23 script:
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24 def this_script_args = (params.fq_single_end ? ' -se' : '')
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25 this_script_args += (params.fq_suffix ? " -r1 '${params.fq_suffix}'" : '')
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26 this_script_args += (params.fq2_suffix ? " -r2 '${params.fq2_suffix}'" : '')
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27
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28 """
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29 fastq_dir_to_samplesheet.py -sn \\
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30 -st '${params.fq_strandedness}' \\
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31 -sd '${params.fq_filename_delim}' \\
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32 -si ${params.fq_filename_delim_idx} \\
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33 ${this_script_args} \\
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34 ${inputdir} autogen_samplesheet.csv
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35
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36 cat <<-END_VERSIONS > versions.yml
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37 "${task.process}":
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38 python: \$( python --version | sed 's/Python //g' )
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39 END_VERSIONS
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40 """
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41 } |
