Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/download_pubmlst_scheme/main.nf @ 14:9e80528263c4
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 17:32:05 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process DOWNLOAD_PUBMLST_SCHEME { |
| kkonganti@11 | 2 tag "dl_pubmlst_profiles_and_schemes.py" |
| kkonganti@11 | 3 label "process_pico" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : |
| kkonganti@11 | 9 'quay.io/biocontainers/python:3.10.4' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 val organism |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 path "${organism}" , emit: pubmlst_dir |
| kkonganti@11 | 16 path 'versions.yml', emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 task.ext.when == null || task.ext.when |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 """ |
| kkonganti@11 | 24 dl_pubmlst_profiles_and_schemes.py \\ |
| kkonganti@11 | 25 -f \\ |
| kkonganti@11 | 26 $args |
| kkonganti@11 | 27 |
| kkonganti@11 | 28 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 29 "${task.process}": |
| kkonganti@11 | 30 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 31 END_VERSIONS |
| kkonganti@11 | 32 """ |
| kkonganti@11 | 33 |
| kkonganti@11 | 34 } |