Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch
comparison 0.2.0/modules/gen_samplesheet/main.nf @ 0:9e8b1c747a6a draft default tip
planemo upload
| author | galaxytrakr |
|---|---|
| date | Fri, 29 May 2026 13:32:17 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:9e8b1c747a6a |
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| 1 process GEN_SAMPLESHEET { | |
| 2 tag "${inputdir.simpleName}" | |
| 3 label "process_pico" | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::python=3.9.5" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/python:3.9--1' : | |
| 9 'quay.io/biocontainers/python:3.9--1' }" | |
| 10 | |
| 11 input: | |
| 12 val inputdir | |
| 13 | |
| 14 output: | |
| 15 path '*.csv' , emit: csv | |
| 16 path 'versions.yml', emit: versions | |
| 17 | |
| 18 when: | |
| 19 task.ext.when == null || task.ext.when | |
| 20 | |
| 21 // This script (fastq_dir_to_samplesheet.py) is distributed | |
| 22 // as part of the pipeline nf-core/rnaseq/bin/. MIT License. | |
| 23 script: | |
| 24 def this_script_args = (params.fq_single_end ? ' -se' : '') | |
| 25 this_script_args += (params.fq_suffix ? " -r1 '${params.fq_suffix}'" : '') | |
| 26 this_script_args += (params.fq2_suffix ? " -r2 '${params.fq2_suffix}'" : '') | |
| 27 | |
| 28 """ | |
| 29 fastq_dir_to_samplesheet.py -sn \\ | |
| 30 -st '${params.fq_strandedness}' \\ | |
| 31 -sd '${params.fq_filename_delim}' \\ | |
| 32 -si ${params.fq_filename_delim_idx} \\ | |
| 33 ${this_script_args} \\ | |
| 34 ${inputdir} autogen_samplesheet.csv | |
| 35 | |
| 36 cat <<-END_VERSIONS > versions.yml | |
| 37 "${task.process}": | |
| 38 python: \$( python --version | sed 's/Python //g' ) | |
| 39 END_VERSIONS | |
| 40 """ | |
| 41 } |