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comparison 0.2.0/modules/prokka/main.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process PROKKA {
2 tag "$meta.id"
3 label 'process_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}prokka${params.fs}1.14.5" : null)
6 conda (params.enable_conda ? "bioconda::prokka=1.14.6 conda-forge::perl" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' :
9 'quay.io/biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
10
11 input:
12 tuple val(meta), path(fasta), path(proteins), path(prodigal_tf)
13
14 output:
15 tuple val(meta), path("${prefix}/*.gff"), emit: gff
16 tuple val(meta), path("${prefix}/*.gbk"), emit: gbk
17 tuple val(meta), path("${prefix}/*.fna"), emit: fna
18 tuple val(meta), path("${prefix}/*.faa"), emit: faa
19 tuple val(meta), path("${prefix}/*.ffn"), emit: ffn
20 tuple val(meta), path("${prefix}/*.sqn"), emit: sqn
21 tuple val(meta), path("${prefix}/*.fsa"), emit: fsa
22 tuple val(meta), path("${prefix}/*.tbl"), emit: tbl
23 tuple val(meta), path("${prefix}/*.err"), emit: err
24 tuple val(meta), path("${prefix}/*.log"), emit: log
25 tuple val(meta), path("${prefix}/*.txt"), emit: txt
26 tuple val(meta), path("${prefix}/*.tsv"), emit: tsv
27 path "versions.yml" , emit: versions
28
29 when:
30 task.ext.when == null || task.ext.when
31
32 script:
33 def args = task.ext.args ?: ''
34 def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
35 def prodigal_tf = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
36 def prefix_l = "${meta.id}" ?: ''
37 prefix = task.ext.prefix ?: "${meta.id}"
38 def strain = !params.prokka_strain && prefix_l ? "--strain '${prefix_l}'" : ''
39
40 """
41 prokka \\
42 $strain \\
43 $args \\
44 --cpus $task.cpus \\
45 --prefix $prefix \\
46 $proteins_opt \\
47 $prodigal_tf \\
48 $fasta
49
50 cat <<-END_VERSIONS > versions.yml
51 "${task.process}":
52 prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
53 END_VERSIONS
54 """
55 }