Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/modules/otf_genome/main.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
9 'quay.io/biocontainers/python:3.10.4' }"
10
11 input:
12 tuple val(meta), path(kma_hits)
13
14 output:
15 tuple val(meta), path('*_scaffolded_genomic.fna.gz'), emit: genomes_fasta, optional: true
16 path '*FAILED.txt' , emit: failed, optional: true
17 path 'versions.yml' , emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 args += (kma_hits ? " -txt ${kma_hits}" : '')
26 args += (params.tuspy_gd ? " -gd ${params.tuspy_gd}" : '')
27 args += (prefix ? " -op ${prefix}" : '')
28
29 """
30 gen_otf_genome.py \\
31 $args
32
33 cat <<-END_VERSIONS > versions.yml
34 "${task.process}":
35 python: \$( python --version | sed 's/Python //g' )
36 END_VERSIONS
37 """
38 }