Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/mlst/main.nf @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 process MLST { |
| kkonganti@101 | 2 tag "$meta.id" |
| kkonganti@101 | 3 label 'process_low' |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mlst${params.fs}2.19.0" : null) |
| kkonganti@101 | 6 conda (params.enable_conda ? "bioconda::mlst=2.19.0" : null) |
| kkonganti@101 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@101 | 8 'https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1' : |
| kkonganti@101 | 9 'quay.io/biocontainers/mlst:2.19.0--hdfd78af_1' }" |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 input: |
| kkonganti@101 | 12 tuple val(meta), path(fasta) |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 output: |
| kkonganti@101 | 15 tuple val(meta), path("*.tsv"), emit: tsv |
| kkonganti@101 | 16 path "versions.yml" , emit: versions |
| kkonganti@101 | 17 |
| kkonganti@101 | 18 when: |
| kkonganti@101 | 19 (task.ext.when == null || task.ext.when) && fasta.size() > 0 |
| kkonganti@101 | 20 |
| kkonganti@101 | 21 script: |
| kkonganti@101 | 22 def args = task.ext.args ?: '' |
| kkonganti@101 | 23 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@101 | 24 """ |
| kkonganti@101 | 25 mlst \\ |
| kkonganti@101 | 26 --threads $task.cpus \\ |
| kkonganti@101 | 27 $args \\ |
| kkonganti@101 | 28 $fasta > ${prefix}.tsv |
| kkonganti@101 | 29 |
| kkonganti@101 | 30 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 31 "${task.process}": |
| kkonganti@101 | 32 mlst: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' ) |
| kkonganti@101 | 33 END_VERSIONS |
| kkonganti@101 | 34 """ |
| kkonganti@101 | 35 |
| kkonganti@101 | 36 } |