Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.2.0/modules/custom/qual_passed_genomes/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 QUAL_PASSED_GENOMES {
2 tag "Consolidate"
3 label "process_micro"
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 acc_passed_tool1
13 path acc_passed_tool2
14
15 output:
16 path 'accs_passed.txt', emit: accs
17 path 'versions.yml' , emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.index ?: ''
25 def output = 'accs_passed.txt'
26
27 """
28 qual_confirm.py \\
29 -f1 $acc_passed_tool1 \\
30 -f2 $acc_passed_tool2
31
32 cat <<-END_VERSIONS >> versions.yml
33 python: \$( python --version | sed 's/Python //g' )
34 END_VERSIONS
35 """
36 }