Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/gen_samplesheet/main.nf @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 process GEN_SAMPLESHEET { |
| kkonganti@101 | 2 tag "${inputdir.simpleName}" |
| kkonganti@101 | 3 label "process_pico" |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@101 | 6 conda (params.enable_conda ? "conda-forge::python=3.9.5" : null) |
| kkonganti@101 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@101 | 8 'https://depot.galaxyproject.org/singularity/python:3.9--1' : |
| kkonganti@101 | 9 'quay.io/biocontainers/python:3.9--1' }" |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 input: |
| kkonganti@101 | 12 val inputdir |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 output: |
| kkonganti@101 | 15 path '*.csv' , emit: csv |
| kkonganti@101 | 16 path 'versions.yml', emit: versions |
| kkonganti@101 | 17 |
| kkonganti@101 | 18 when: |
| kkonganti@101 | 19 task.ext.when == null || task.ext.when |
| kkonganti@101 | 20 |
| kkonganti@101 | 21 // This script (fastq_dir_to_samplesheet.py) is distributed |
| kkonganti@101 | 22 // as part of the pipeline nf-core/rnaseq/bin/. MIT License. |
| kkonganti@101 | 23 script: |
| kkonganti@101 | 24 def this_script_args = (params.fq_single_end ? ' -se' : '') |
| kkonganti@101 | 25 this_script_args += (params.fq_suffix ? " -r1 '${params.fq_suffix}'" : '') |
| kkonganti@101 | 26 this_script_args += (params.fq2_suffix ? " -r2 '${params.fq2_suffix}'" : '') |
| kkonganti@101 | 27 |
| kkonganti@101 | 28 """ |
| kkonganti@101 | 29 fastq_dir_to_samplesheet.py -sn \\ |
| kkonganti@101 | 30 -st '${params.fq_strandedness}' \\ |
| kkonganti@101 | 31 -sd '${params.fq_filename_delim}' \\ |
| kkonganti@101 | 32 -si ${params.fq_filename_delim_idx} \\ |
| kkonganti@101 | 33 ${this_script_args} \\ |
| kkonganti@101 | 34 ${inputdir} autogen_samplesheet.csv |
| kkonganti@101 | 35 |
| kkonganti@101 | 36 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 37 "${task.process}": |
| kkonganti@101 | 38 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@101 | 39 END_VERSIONS |
| kkonganti@101 | 40 """ |
| kkonganti@101 | 41 } |