Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.6.1/modules/abricate/run/main.nf @ 11:749faef1caa9

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"planemo upload"
author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
1 process ABRICATE_RUN {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}abricate${params.fs}1.0.1" : null)
6 conda (params.enable_conda ? "conda-forge::perl bioconda::abricate=1.0.1" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
9 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
10
11 input:
12 tuple val(meta), path(assembly)
13 val abdbs
14
15 output:
16 path "${meta.id}${params.fs}*"
17 tuple val(meta), path("${meta.id}${params.fs}*.ab.txt"), emit: abricated
18 path "versions.yml" , emit: versions
19
20 when:
21 (task.ext.when == null || task.ext.when) && assembly.size() > 0
22
23 script:
24 def args = task.ext.args ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}"
26 def dbs = abdbs.collect().join('\\n')
27 """
28 newprefix="${prefix}${params.fs}${prefix}"
29
30 if [ ! -d "$prefix" ]; then
31 mkdir "$prefix" || exit 1
32 fi
33
34 echo -e "$dbs" | while read -r db; do
35 abricate \\
36 $assembly \\
37 $args \\
38 --db \$db \\
39 --threads $task.cpus 1> "\${newprefix}.\${db}.ab.txt"
40 done
41
42 cat <<-END_VERSIONS > versions.yml
43 "${task.process}":
44 abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
45 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
46 END_VERSIONS
47 """
48 }