Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/index_pdg_metadata/main.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process INDEX_PDG_METADATA {
2 tag "index_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 path pdg_metadata
13 path pdg_ref_snp_metadata
14 path accs_all
15 path mlst_results
16
17 output:
18 path "*.pickle" , emit: index
19 path 'versions.yml', emit: versions
20
21 when:
22 task.ext.when == null || task.ext.when
23
24 script:
25 def args = task.ext.args ?: ''
26 def mlst_results = (mlst_results ? "-mlst ${mlst_results}" : '')
27 """
28 index_pdg_metadata.py \\
29 $mlst_results \\
30 -pdg_dir "."
31
32 cat <<-END_VERSIONS > versions.yml
33 "${task.process}":
34 python: \$( python --version | sed 's/Python //g' )
35 END_VERSIONS
36 """
37
38 }