Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/modules/salmon/index/main.nf @ 11:749faef1caa9
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:51:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process SALMON_INDEX { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label "process_micro" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}salmon${params.fs}1.10.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? 'conda-forge::libgcc-ng bioconda::salmon=1.10.1' : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_1' : |
| kkonganti@11 | 9 'quay.io/biocontainers/salmon:1.10.1--h7e5ed60_1' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(genome_fasta) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("${meta.id}_salmon_idx"), emit: idx |
| kkonganti@11 | 16 path "versions.yml" , emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 task.ext.when == null || task.ext.when |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 def prefix = task.ext.prefix ?: "${meta.id}_salmon_idx" |
| kkonganti@11 | 24 def decoys_file = file( meta.salmon_decoys ) |
| kkonganti@11 | 25 def decoys = !("${decoys_file.simpleName}" ==~ 'dummy_file.*') && decoys_file.exits() ? "--decoys ${meta.salmon_decoys}" : '' |
| kkonganti@11 | 26 """ |
| kkonganti@11 | 27 salmon \\ |
| kkonganti@11 | 28 index \\ |
| kkonganti@11 | 29 $decoys \\ |
| kkonganti@11 | 30 --threads $task.cpus \\ |
| kkonganti@11 | 31 $args \\ |
| kkonganti@11 | 32 --index $prefix \\ |
| kkonganti@11 | 33 --transcripts $genome_fasta |
| kkonganti@11 | 34 |
| kkonganti@11 | 35 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 36 "${task.process}": |
| kkonganti@11 | 37 salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g") |
| kkonganti@11 | 38 END_VERSIONS |
| kkonganti@11 | 39 """ |
| kkonganti@11 | 40 } |