Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/rmlst/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 RMLST_POST {
2 tag "${meta.id}"
3 label "process_pico"
4 maxForks 3
5
6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
7 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::requests" : null)
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
9 'https://depot.galaxyproject.org/singularity/requests:2.26.0' :
10 'quay.io/biocontainers/requests:2.26.0' }"
11
12 input:
13 tuple val(meta), path(genome)
14
15 output:
16 tuple val(meta), path('*.tsv') , emit: tsv, optional: true
17 tuple val(meta), path('*.log.json'), emit: log, optional: true
18 path 'versions.yml' , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def prefix = (task.ext.prefix ?: meta.id)
25
26 """
27 rmlst_post.py \\
28 -fasta $genome \\
29 -prefix $prefix \\
30
31 cat <<-END_VERSIONS > versions.yml
32 "${task.process}":
33 python: \$( python --version | sed 's/Python //g' )
34 requests: \$( python -c "import requests; print (requests.__version__)" )
35 END_VERSIONS
36 """
37 }