Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/modules/mlst/main.nf @ 0:c8597e9e1a97
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 12:37:44 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process MLST { |
| kkonganti@0 | 2 tag "$meta.id" |
| kkonganti@0 | 3 label 'process_micro' |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.23.0" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? "conda-forge::perl bioconda::mlst=2.23.0" : null) |
| kkonganti@0 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@0 | 8 'https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1' : |
| kkonganti@0 | 9 'quay.io/biocontainers/mlst:2.23.0--hdfd78af_1' }" |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 input: |
| kkonganti@0 | 12 tuple val(meta), path(fasta), path(datadir) |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 output: |
| kkonganti@0 | 15 tuple val(meta), path("*.tsv"), emit: tsv |
| kkonganti@0 | 16 path "versions.yml" , emit: versions |
| kkonganti@0 | 17 |
| kkonganti@0 | 18 when: |
| kkonganti@0 | 19 (task.ext.when == null || task.ext.when) && fasta.size() > 0 |
| kkonganti@0 | 20 |
| kkonganti@0 | 21 script: |
| kkonganti@0 | 22 def args = task.ext.args ?: '' |
| kkonganti@0 | 23 def prefix = (task.ext.prefix ?: "${meta.id}") + (task.index ?: '') |
| kkonganti@0 | 24 def label = (params.mlst_label ? "--label '${prefix}'" : '') |
| kkonganti@0 | 25 args += (datadir ? " --datadir '.' " : '') |
| kkonganti@0 | 26 """ |
| kkonganti@0 | 27 mlst \\ |
| kkonganti@0 | 28 --threads $task.cpus \\ |
| kkonganti@0 | 29 $label \\ |
| kkonganti@0 | 30 $args \\ |
| kkonganti@0 | 31 $fasta > ${prefix}.tsv |
| kkonganti@0 | 32 |
| kkonganti@0 | 33 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 34 "${task.process}": |
| kkonganti@0 | 35 mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' ) |
| kkonganti@0 | 36 END_VERSIONS |
| kkonganti@0 | 37 """ |
| kkonganti@0 | 38 |
| kkonganti@0 | 39 } |