Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/samplesheet_check/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 SAMPLESHEET_CHECK { |
| kkonganti@101 | 2 tag "$samplesheet" |
| kkonganti@101 | 3 label "process_femto" |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 module (params.enable_module ? "${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 path samplesheet |
| 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 script: // This script is bundled with the pipeline, in nf-core/rnaseq/bin/ |
| kkonganti@101 | 22 """ |
| kkonganti@101 | 23 check_samplesheet.py \\ |
| kkonganti@101 | 24 $samplesheet \\ |
| kkonganti@101 | 25 samplesheet.valid.csv |
| kkonganti@101 | 26 |
| kkonganti@101 | 27 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 28 "${task.process}": |
| kkonganti@101 | 29 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@101 | 30 END_VERSIONS |
| kkonganti@101 | 31 """ |
| kkonganti@101 | 32 } |