Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.2.0/modules/download_pdg_metadata/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_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 args += (params.pdg_org ? " -org ${params.pdg_org}" : '')
27 """
28 dl_pdg_metadata.py \\
29 $args
30
31 cat <<-END_VERSIONS > versions.yml
32 "${task.process}":
33 python: \$( python --version | sed 's/Python //g' )
34 END_VERSIONS
35 """
36
37 }