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comparison 0.2.0/modules/pirate/main.nf @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 process PIRATE {
2 tag "$meta.id"
3 label 'process_medium'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}pirate${params.fs}5.2.0" : null)
6 conda (params.enable_conda ? "bioconda::pirate=1.0.5 bioconda::mcl=14.137 conda-forge::r-dplyr" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/pirate:1.0.5--hdfd78af_0' :
9 'quay.io/biocontainers/pirate:1.0.5--hdfd78af_0' }"
10
11 input:
12 tuple val(meta), path(gff)
13
14 output:
15 tuple val(meta), path("results/*") , emit: results
16 tuple val(meta), path("results/core_alignment.fasta"), emit: aln, optional: true
17 path "versions.yml" , emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 def rplots = (params.enable_conda ? '--rplots' : '')
26 """
27 PIRATE \\
28 $args \\
29 $rplots \\
30 --threads $task.cpus \\
31 --input ".${params.fs}" \\
32 --output results/
33
34 cat <<-END_VERSIONS > versions.yml
35 "${task.process}":
36 pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' )
37 END_VERSIONS
38 """
39 }