Mercurial > repos > kkonganti > cfsan_bettercallsal
comparison 0.6.1/modules/otf_genome/main.nf @ 11:749faef1caa9
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:51:40 -0400 |
| parents | |
| children |
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| 10:1b9de878b04a | 11:749faef1caa9 |
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| 1 process OTF_GENOME { | |
| 2 tag "$meta.id" | |
| 3 label "process_pico" | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : | |
| 9 'quay.io/biocontainers/python:3.10.4' }" | |
| 10 | |
| 11 input: | |
| 12 tuple val(meta), path(kma_hits), path(kma_fragz) | |
| 13 | |
| 14 output: | |
| 15 tuple val(meta), path('*_scaffolded_genomic.fna.gz'), emit: genomes_fasta, optional: true | |
| 16 tuple val(meta), path('*_aln_reads.fna.gz') , emit: reads_extracted, optional: true | |
| 17 path '*FAILED.txt' , emit: failed, optional: true | |
| 18 path 'versions.yml' , emit: versions | |
| 19 | |
| 20 when: | |
| 21 task.ext.when == null || task.ext.when | |
| 22 | |
| 23 script: | |
| 24 def args = task.ext.args ?: '' | |
| 25 def prefix = task.ext.prefix ?: "${meta.id}" | |
| 26 args += (kma_hits ? " -txt ${kma_hits}" : '') | |
| 27 args += (params.tuspy_gd ? " -gd ${params.tuspy_gd}" : '') | |
| 28 args += (prefix ? " -op ${prefix}" : '') | |
| 29 | |
| 30 """ | |
| 31 gen_otf_genome.py \\ | |
| 32 $args | |
| 33 | |
| 34 cat <<-END_VERSIONS > versions.yml | |
| 35 "${task.process}": | |
| 36 python: \$( python --version | sed 's/Python //g' ) | |
| 37 END_VERSIONS | |
| 38 """ | |
| 39 } |