Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch
comparison 0.2.0/modules/download_pubmlst_scheme/main.nf @ 0:9e8b1c747a6a draft default tip
planemo upload
| author | galaxytrakr |
|---|---|
| date | Fri, 29 May 2026 13:32:17 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:9e8b1c747a6a |
|---|---|
| 1 process DOWNLOAD_PUBMLST_SCHEME { | |
| 2 tag "dl_pubmlst_profiles_and_schemes.py" | |
| 3 label "process_pico" | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : | |
| 9 'quay.io/biocontainers/python:3.10.4' }" | |
| 10 | |
| 11 input: | |
| 12 val organism | |
| 13 | |
| 14 output: | |
| 15 path "${organism}" , emit: pubmlst_dir | |
| 16 path 'versions.yml', emit: versions | |
| 17 | |
| 18 when: | |
| 19 task.ext.when == null || task.ext.when | |
| 20 | |
| 21 script: | |
| 22 def args = task.ext.args ?: '' | |
| 23 """ | |
| 24 dl_pubmlst_profiles_and_schemes.py \\ | |
| 25 -f \\ | |
| 26 $args | |
| 27 | |
| 28 cat <<-END_VERSIONS > versions.yml | |
| 29 "${task.process}": | |
| 30 python: \$( python --version | sed 's/Python //g' ) | |
| 31 END_VERSIONS | |
| 32 """ | |
| 33 | |
| 34 } |