Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.2.0/modules/download_pubmlst_scheme/main.nf @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
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 }