kkonganti@11: process GEN_SAMPLESHEET {
kkonganti@11:     tag "${inputdir.simpleName}"
kkonganti@11:     label "process_pico"
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::python=3.9.5" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/python:3.9--1' :
kkonganti@11:         'quay.io/biocontainers/python:3.9--1' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         val inputdir
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         path '*.csv'       , emit: csv
kkonganti@11:         path 'versions.yml', emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     // This script (fastq_dir_to_samplesheet.py) is distributed
kkonganti@11:     // as part of the pipeline nf-core/rnaseq/bin/. MIT License.
kkonganti@11:     script:
kkonganti@11:         def this_script_args = (params.fq_single_end ? ' -se' : '')
kkonganti@11:         this_script_args += (params.fq_suffix ? " -r1 '${params.fq_suffix}'" : '')
kkonganti@11:         this_script_args += (params.fq2_suffix ? " -r2 '${params.fq2_suffix}'" : '')
kkonganti@11: 
kkonganti@11:         """
kkonganti@11:         fastq_dir_to_samplesheet.py -sn \\
kkonganti@11:             -st '${params.fq_strandedness}' \\
kkonganti@11:             -sd '${params.fq_filename_delim}' \\
kkonganti@11:             -si ${params.fq_filename_delim_idx} \\
kkonganti@11:             ${this_script_args} \\
kkonganti@11:             ${inputdir} autogen_samplesheet.csv
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             python: \$( python --version | sed 's/Python //g' )
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: }