Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.2/modules/mlst/main.nf @ 105:52045ea4679d

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"planemo upload"
author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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104:17890124001d 105:52045ea4679d
1 process MLST {
2 tag "$meta.id"
3 label 'process_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.19.0" : null)
6 conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' :
9 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }"
10
11 input:
12 tuple val(meta), path(fasta)
13
14 output:
15 tuple val(meta), path("*.tsv"), emit: tsv
16 path "versions.yml" , emit: versions
17
18 when:
19 (task.ext.when == null || task.ext.when) && fasta.size() > 0
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24 """
25 mlst \\
26 --threads $task.cpus \\
27 $args \\
28 $fasta > ${prefix}.tsv
29
30 cat <<-END_VERSIONS > versions.yml
31 "${task.process}":
32 mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
33 END_VERSIONS
34 """
35
36 }