Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/modules/salmon/index/main.nf @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 process SALMON_INDEX {
2 tag "$meta.id"
3 label "process_micro"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}salmon${params.fs}1.10.0" : null)
6 conda (params.enable_conda ? 'conda-forge::libgcc-ng bioconda::salmon=1.10.1' : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_1' :
9 'quay.io/biocontainers/salmon:1.10.1--h7e5ed60_1' }"
10
11 input:
12 tuple val(meta), path(genome_fasta)
13
14 output:
15 tuple val(meta), path("${meta.id}_salmon_idx"), emit: idx
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}_salmon_idx"
24 def decoys_file = file( meta.salmon_decoys )
25 def decoys = !("${decoys_file.simpleName}" ==~ 'dummy_file.*') && decoys_file.exits() ? "--decoys ${meta.salmon_decoys}" : ''
26 """
27 salmon \\
28 index \\
29 $decoys \\
30 --threads $task.cpus \\
31 $args \\
32 --index $prefix \\
33 --transcripts $genome_fasta
34
35 cat <<-END_VERSIONS > versions.yml
36 "${task.process}":
37 salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
38 END_VERSIONS
39 """
40 }