Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/mlst/main.nf @ 17:b571995ddb51
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 19:01:29 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process MLST { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_micro' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.23.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::perl bioconda::mlst=2.23.0" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1' : |
| kkonganti@11 | 9 'quay.io/biocontainers/mlst:2.23.0--hdfd78af_1' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(fasta), path(datadir) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("*.tsv"), emit: tsv |
| kkonganti@11 | 16 path "versions.yml" , emit: versions |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 when: |
| kkonganti@11 | 19 (task.ext.when == null || task.ext.when) && fasta.size() > 0 |
| kkonganti@11 | 20 |
| kkonganti@11 | 21 script: |
| kkonganti@11 | 22 def args = task.ext.args ?: '' |
| kkonganti@11 | 23 def taskid = (task.index ?: '') |
| kkonganti@11 | 24 def prefix = (meta.id ?: 'MLST' + taskid.toString()) |
| kkonganti@11 | 25 def label = (params.mlst_label ? "--label '${prefix}'" : '') |
| kkonganti@11 | 26 args += (datadir ? " --datadir '.' " : '') |
| kkonganti@11 | 27 """ |
| kkonganti@11 | 28 mlst \\ |
| kkonganti@11 | 29 --threads $task.cpus \\ |
| kkonganti@11 | 30 $label \\ |
| kkonganti@11 | 31 $args \\ |
| kkonganti@11 | 32 $fasta > ${prefix}.tsv |
| kkonganti@11 | 33 |
| kkonganti@11 | 34 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 35 "${task.process}": |
| kkonganti@11 | 36 mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' ) |
| kkonganti@11 | 37 END_VERSIONS |
| kkonganti@11 | 38 """ |
| kkonganti@11 | 39 |
| kkonganti@11 | 40 } |