Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.3.0/modules/seqsero2/main.nf @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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91:046e57368d3b 92:295c2597a475
1 process SEQSERO2 {
2 tag "$meta.id"
3 label 'process_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqsero2${params.fs}1.2.1" : null)
6 conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' :
9 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }"
10
11 input:
12 tuple val(meta), path(reads_or_asm)
13
14 output:
15 path("${meta.id}${params.fs}*")
16 tuple val(meta), path("${meta.id}${params.fs}*_result.tsv"), emit: serotyped
17 path "versions.yml" , emit: versions
18
19 when:
20 (task.ext.when == null || task.ext.when) && reads_or_asm.size() > 0
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 """
26 SeqSero2_package.py \\
27 $args \\
28 -d $prefix \\
29 -n $prefix \\
30 -p $task.cpus \\
31 -i $reads_or_asm
32
33 mv ${prefix}${params.fs}SeqSero_log.txt ${prefix}${params.fs}${prefix}.SeqSero_log.txt
34 mv ${prefix}${params.fs}SeqSero_result.txt ${prefix}${params.fs}${prefix}.SeqSero_result.txt
35 mv ${prefix}${params.fs}SeqSero_result.tsv ${prefix}${params.fs}${prefix}.SeqSero_result.tsv
36
37 cat <<-END_VERSIONS > versions.yml
38 "${task.process}":
39 seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' )
40 END_VERSIONS
41 """
42 }