Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.1.0/modules/mlst/main.nf @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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-1:000000000000 0:c8597e9e1a97
1 process MLST {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.23.0" : null)
6 conda (params.enable_conda ? "conda-forge::perl bioconda::mlst=2.23.0" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1' :
9 'quay.io/biocontainers/mlst:2.23.0--hdfd78af_1' }"
10
11 input:
12 tuple val(meta), path(fasta), path(datadir)
13
14 output:
15 tuple val(meta), path("*.tsv"), emit: tsv
16 path "versions.yml" , emit: versions
17
18 when:
19 (task.ext.when == null || task.ext.when) && fasta.size() > 0
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = (task.ext.prefix ?: "${meta.id}") + (task.index ?: '')
24 def label = (params.mlst_label ? "--label '${prefix}'" : '')
25 args += (datadir ? " --datadir '.' " : '')
26 """
27 mlst \\
28 --threads $task.cpus \\
29 $label \\
30 $args \\
31 $fasta > ${prefix}.tsv
32
33 cat <<-END_VERSIONS > versions.yml
34 "${task.process}":
35 mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
36 END_VERSIONS
37 """
38
39 }