Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/modules/otf_genome/main.nf @ 12:c5faadb3386f
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:57:15 -0400 |
| parents | 749faef1caa9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process OTF_GENOME { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label "process_pico" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/python:3.10.4' : |
| kkonganti@11 | 9 'quay.io/biocontainers/python:3.10.4' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(kma_hits), path(kma_fragz) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path('*_scaffolded_genomic.fna.gz'), emit: genomes_fasta, optional: true |
| kkonganti@11 | 16 tuple val(meta), path('*_aln_reads.fna.gz') , emit: reads_extracted, optional: true |
| kkonganti@11 | 17 path '*FAILED.txt' , emit: failed, optional: true |
| kkonganti@11 | 18 path 'versions.yml' , emit: versions |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 when: |
| kkonganti@11 | 21 task.ext.when == null || task.ext.when |
| kkonganti@11 | 22 |
| kkonganti@11 | 23 script: |
| kkonganti@11 | 24 def args = task.ext.args ?: '' |
| kkonganti@11 | 25 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@11 | 26 args += (kma_hits ? " -txt ${kma_hits}" : '') |
| kkonganti@11 | 27 args += (params.tuspy_gd ? " -gd ${params.tuspy_gd}" : '') |
| kkonganti@11 | 28 args += (prefix ? " -op ${prefix}" : '') |
| kkonganti@11 | 29 |
| kkonganti@11 | 30 """ |
| kkonganti@11 | 31 gen_otf_genome.py \\ |
| kkonganti@11 | 32 $args |
| kkonganti@11 | 33 |
| kkonganti@11 | 34 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 35 "${task.process}": |
| kkonganti@11 | 36 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@11 | 37 END_VERSIONS |
| kkonganti@11 | 38 """ |
| kkonganti@11 | 39 } |