Mercurial > repos > kkonganti > cfsan_cronology
comparison 0.2.0/modules/mash/paste/main.nf @ 11:a5f31c44f8c9
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:11:44 -0400 |
| parents | |
| children |
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| 10:ddf7a172bf30 | 11:a5f31c44f8c9 |
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| 1 process MASH_PASTE { | |
| 2 tag "${meta.id}" | |
| 3 label 'process_low' | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mash${params.fs}2.3" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1': | |
| 9 'quay.io/biocontainers/mash:2.3--he348c14_1' }" | |
| 10 | |
| 11 input: | |
| 12 tuple val(meta), path(sketch) | |
| 13 | |
| 14 output: | |
| 15 tuple val(meta), path("*.msh") , emit: sketch | |
| 16 tuple val(meta), path("*_mash_sketch.status"), emit: stats | |
| 17 path "versions.yml" , emit: versions | |
| 18 | |
| 19 when: | |
| 20 task.ext.when == null || task.ext.when | |
| 21 | |
| 22 script: | |
| 23 def args = task.ext.args ?: '' | |
| 24 def prefix = task.ext.prefix ?: "${meta.id}" | |
| 25 def sketches = (sketch ? sketch.collect().join('\\n') : null) | |
| 26 """ | |
| 27 echo -e "$sketches" > paste_these.txt | |
| 28 | |
| 29 mash \\ | |
| 30 paste \\ | |
| 31 "msh.k${params.mashsketch_k}.${params.mashsketch_s}h.${prefix}" \\ | |
| 32 -l paste_these.txt \\ | |
| 33 2> ${prefix}_mash_sketch.status | |
| 34 | |
| 35 cat <<-END_VERSIONS > versions.yml | |
| 36 "${task.process}": | |
| 37 mash: \$( mash --version ) | |
| 38 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) | |
| 39 END_VERSIONS | |
| 40 """ | |
| 41 } |