Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/polypolish/main.nf @ 12:78a02e8cb092
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:16:59 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process POLYPOLISH { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_micro' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}polypolish${params.fs}0.5.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "bioconda::polypolish=0.5.0 conda-forge::libgcc-ng" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/polypolish:0.5.0--hdbdd923_4' : |
| kkonganti@11 | 9 'quay.io/biocontainers/polypolish:0.5.0--hdbdd923_4' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(genome), path(sam) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("*.polished.fa"), emit: polished |
| kkonganti@11 | 16 path "versions.yml" , emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 task.ext.when == null || task.ext.when |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@11 | 24 """ |
| kkonganti@11 | 25 |
| kkonganti@11 | 26 polypolish \\ |
| kkonganti@11 | 27 $args \\ |
| kkonganti@11 | 28 $genome \\ |
| kkonganti@11 | 29 ${sam.join(' ')} > ${prefix}.polished.fa |
| kkonganti@11 | 30 |
| kkonganti@11 | 31 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 32 "${task.process}": |
| kkonganti@11 | 33 polypolish: \$(echo \$(polypolish -V 2>&1) | sed 's/^Polypolish v//') |
| kkonganti@11 | 34 END_VERSIONS |
| kkonganti@11 | 35 """ |
| kkonganti@11 | 36 } |