Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/modules/seqsero2/main.nf @ 143:620bffa66bbb tip
planemo upload
| author | kkonganti |
|---|---|
| date | Thu, 11 Jul 2024 14:48:07 -0400 |
| parents | 52045ea4679d |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 process SEQSERO2 { |
| kkonganti@105 | 2 tag "$meta.id" |
| kkonganti@105 | 3 label 'process_low' |
| kkonganti@105 | 4 |
| kkonganti@105 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqsero2${params.fs}1.2.1" : null) |
| kkonganti@105 | 6 conda (params.enable_conda ? "bioconda::seqsero2=1.2.1" : null) |
| kkonganti@105 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@105 | 8 'https://depot.galaxyproject.org/singularity/seqsero2:1.2.1--py_0' : |
| kkonganti@105 | 9 'quay.io/biocontainers/seqsero2:1.2.1--py_0' }" |
| kkonganti@105 | 10 |
| kkonganti@105 | 11 input: |
| kkonganti@105 | 12 tuple val(meta), path(reads_or_asm) |
| kkonganti@105 | 13 |
| kkonganti@105 | 14 output: |
| kkonganti@105 | 15 path("${meta.id}${params.fs}*") |
| kkonganti@105 | 16 tuple val(meta), path("${meta.id}${params.fs}*_result.tsv"), emit: serotyped |
| kkonganti@105 | 17 path "versions.yml" , emit: versions |
| kkonganti@105 | 18 |
| kkonganti@105 | 19 when: |
| kkonganti@105 | 20 (task.ext.when == null || task.ext.when) && reads_or_asm.size() > 0 |
| kkonganti@105 | 21 |
| kkonganti@105 | 22 script: |
| kkonganti@105 | 23 def args = task.ext.args ?: '' |
| kkonganti@105 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@105 | 25 """ |
| kkonganti@105 | 26 SeqSero2_package.py \\ |
| kkonganti@105 | 27 $args \\ |
| kkonganti@105 | 28 -d $prefix \\ |
| kkonganti@105 | 29 -n $prefix \\ |
| kkonganti@105 | 30 -p $task.cpus \\ |
| kkonganti@105 | 31 -i $reads_or_asm |
| kkonganti@105 | 32 |
| kkonganti@105 | 33 mv ${prefix}${params.fs}SeqSero_log.txt ${prefix}${params.fs}${prefix}.SeqSero_log.txt |
| kkonganti@105 | 34 mv ${prefix}${params.fs}SeqSero_result.txt ${prefix}${params.fs}${prefix}.SeqSero_result.txt |
| kkonganti@105 | 35 mv ${prefix}${params.fs}SeqSero_result.tsv ${prefix}${params.fs}${prefix}.SeqSero_result.tsv |
| kkonganti@105 | 36 |
| kkonganti@105 | 37 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 38 "${task.process}": |
| kkonganti@105 | 39 seqsero2: \$( echo \$( SeqSero2_package.py --version 2>&1) | sed 's/^.*SeqSero2_package.py //' ) |
| kkonganti@105 | 40 END_VERSIONS |
| kkonganti@105 | 41 """ |
| kkonganti@105 | 42 } |