Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/modules/top_unique_serovars/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 TOP_UNIQUE_SEROVARS {
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
9 'quay.io/biocontainers/python:3.10.4' }"
10
11 input:
12 tuple val(meta), path(mash_screen_res)
13
14 output:
15 tuple val(meta), path('*_UNIQUE_HITS.txt') , emit: tsv, optional: true
16 tuple val(meta), path('*_UNIQUE_HITS.fna.gz'), emit: genomes_fasta, optional: true
17 path'*FAILED.txt' , emit: failed, optional: true
18 path 'versions.yml' , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}"
26 args += (mash_screen_res ? " -m ${mash_screen_res}" : '')
27 args += (prefix ? " -op ${prefix}" : '')
28 """
29 get_top_unique_mash_hit_genomes.py \\
30 $args
31
32 cat <<-END_VERSIONS > versions.yml
33 "${task.process}":
34 python: \$( python --version | sed 's/Python //g' )
35 END_VERSIONS
36 """
37
38 }