Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/download_pdg_metadata/main.nf @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 process DOWNLOAD_PDG_METADATA {
2 tag "dl_pdg_metadata.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 pdg_release
13
14 output:
15 path "**${params.fs}*.metadata.tsv" , emit: pdg_metadata
16 path "**${params.fs}*.reference_target.cluster_list.tsv", emit: snp_cluster_metadata
17 path "**${params.fs}*accs_all.txt" , emit: accs
18 path 'versions.yml' , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 args += (pdg_release ? " -rel ${pdg_release}" : '')
26 """
27 dl_pdg_metadata.py \\
28 $args
29
30 cat <<-END_VERSIONS > versions.yml
31 "${task.process}":
32 python: \$( python --version | sed 's/Python //g' )
33 END_VERSIONS
34 """
35
36 }