Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/pirate/main.nf @ 18:a72c172df773 tip
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 21:40:42 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process PIRATE { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_medium' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}pirate${params.fs}5.2.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "bioconda::pirate=1.0.5 bioconda::mcl=14.137 conda-forge::r-dplyr" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/pirate:1.0.5--hdfd78af_0' : |
| kkonganti@11 | 9 'quay.io/biocontainers/pirate:1.0.5--hdfd78af_0' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(gff) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("results/*") , emit: results |
| kkonganti@11 | 16 tuple val(meta), path("results/core_alignment.fasta"), emit: aln, optional: true |
| kkonganti@11 | 17 path "versions.yml" , emit: versions |
| kkonganti@11 | 18 |
| kkonganti@11 | 19 when: |
| kkonganti@11 | 20 task.ext.when == null || task.ext.when |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 script: |
| kkonganti@11 | 23 def args = task.ext.args ?: '' |
| kkonganti@11 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@11 | 25 def rplots = (params.enable_conda ? '--rplots' : '') |
| kkonganti@11 | 26 """ |
| kkonganti@11 | 27 PIRATE \\ |
| kkonganti@11 | 28 $args \\ |
| kkonganti@11 | 29 $rplots \\ |
| kkonganti@11 | 30 --threads $task.cpus \\ |
| kkonganti@11 | 31 --input ".${params.fs}" \\ |
| kkonganti@11 | 32 --output results/ |
| kkonganti@11 | 33 |
| kkonganti@11 | 34 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 35 "${task.process}": |
| kkonganti@11 | 36 pirate: \$( echo \$( PIRATE --version 2>&1) | sed 's/PIRATE //' ) |
| kkonganti@11 | 37 END_VERSIONS |
| kkonganti@11 | 38 """ |
| kkonganti@11 | 39 } |