Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.2.1/modules/seqsero2/main.nf @ 0:77494b0fa3c7
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Jun 2022 15:55:37 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process SEQSERO2 { |
| kkonganti@0 | 2 tag "$meta.id" |
| kkonganti@0 | 3 label 'process_low' |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqsero2${params.fs}1.2.1" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) |
| kkonganti@0 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@0 | 8 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : |
| kkonganti@0 | 9 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }" |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 input: |
| kkonganti@0 | 12 tuple val(meta), path(reads_or_asm) |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 output: |
| kkonganti@0 | 15 path("${meta.id}${params.fs}*") |
| kkonganti@0 | 16 tuple val(meta), path("${meta.id}${params.fs}*_result.tsv"), emit: serotyped |
| kkonganti@0 | 17 path "versions.yml" , emit: versions |
| kkonganti@0 | 18 |
| kkonganti@0 | 19 when: |
| kkonganti@0 | 20 (task.ext.when == null || task.ext.when) && reads_or_asm.size() > 0 |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 script: |
| kkonganti@0 | 23 def args = task.ext.args ?: '' |
| kkonganti@0 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@0 | 25 """ |
| kkonganti@0 | 26 SeqSero2_package.py \\ |
| kkonganti@0 | 27 $args \\ |
| kkonganti@0 | 28 -d $prefix \\ |
| kkonganti@0 | 29 -n $prefix \\ |
| kkonganti@0 | 30 -p $task.cpus \\ |
| kkonganti@0 | 31 -i $reads_or_asm |
| kkonganti@0 | 32 |
| kkonganti@0 | 33 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 34 "${task.process}": |
| kkonganti@0 | 35 seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' ) |
| kkonganti@0 | 36 END_VERSIONS |
| kkonganti@0 | 37 """ |
| kkonganti@0 | 38 } |