kkonganti@0: process GEN_SAMPLESHEET { kkonganti@0: tag "${inputdir.simpleName}" kkonganti@0: label "process_pico" kkonganti@0: kkonganti@0: module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) kkonganti@0: conda (params.enable_conda ? "conda-forge::python=3.9.5" : null) kkonganti@0: container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? kkonganti@0: 'https://depot.galaxyproject.org/singularity/python:3.9--1' : kkonganti@0: 'quay.io/biocontainers/python:3.9--1' }" kkonganti@0: kkonganti@0: input: kkonganti@0: val inputdir kkonganti@0: kkonganti@0: output: kkonganti@0: path '*.csv' , emit: csv kkonganti@0: path 'versions.yml', emit: versions kkonganti@0: kkonganti@0: when: kkonganti@0: task.ext.when == null || task.ext.when kkonganti@0: kkonganti@0: // This script (fastq_dir_to_samplesheet.py) is distributed kkonganti@0: // as part of the pipeline nf-core/rnaseq/bin/. MIT License. kkonganti@0: script: kkonganti@0: def this_script_args = (params.fq_single_end ? ' -se' : '') kkonganti@0: this_script_args += (params.fq_suffix ? " -r1 '${params.fq_suffix}'" : '') kkonganti@0: this_script_args += (params.fq2_suffix ? " -r2 '${params.fq2_suffix}'" : '') kkonganti@0: kkonganti@0: """ kkonganti@0: fastq_dir_to_samplesheet.py -sn \\ kkonganti@0: -st '${params.fq_strandedness}' \\ kkonganti@0: -sd '${params.fq_filename_delim}' \\ kkonganti@0: -si ${params.fq_filename_delim_idx} \\ kkonganti@0: ${this_script_args} \\ kkonganti@0: ${inputdir} autogen_samplesheet.csv kkonganti@0: kkonganti@0: cat <<-END_VERSIONS > versions.yml kkonganti@0: "${task.process}": kkonganti@0: python: \$( python --version | sed 's/Python //g' ) kkonganti@0: END_VERSIONS kkonganti@0: """ kkonganti@0: }