Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.7.0/modules/top_unique_serovars/main.nf @ 17:0e7a0053e4a6

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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16:b90e5a7a3d4f 17:0e7a0053e4a6
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
9 'quay.io/biocontainers/python:3.10.4' }"
10
11 input:
12 tuple val(meta), path(mash_screen_res)
13
14 output:
15 tuple val(meta), path('*_UNIQUE_HITS.txt') , emit: tsv, optional: true
16 tuple val(meta), path('*_UNIQUE_HITS_POPUP.txt'), emit: popup, optional: true
17 tuple val(meta), path('*_UNIQUE_HITS_ACCS.txt') , emit: accessions, optional: true
18 tuple val(meta), path('*_UNIQUE_HITS.fna.gz') , emit: genomes_fasta, optional: true
19 path'*FAILED.txt' , emit: failed, optional: true
20 path 'versions.yml' , emit: versions
21
22 when:
23 task.ext.when == null || task.ext.when
24
25 script:
26 def args = task.ext.args ?: ''
27 def prefix = task.ext.prefix ?: "${meta.id}"
28 args += (mash_screen_res ? " -m ${mash_screen_res}" : '')
29 args += (prefix ? " -op ${prefix}" : '')
30 """
31 get_top_unique_mash_hit_genomes.py \\
32 $args
33
34 cat <<-END_VERSIONS > versions.yml
35 "${task.process}":
36 python: \$( python --version | sed 's/Python //g' )
37 datasets: \$( datasets --version | sed 's/datasets version: //g' )
38 dataformat: \$( dataformat version )
39 END_VERSIONS
40 """
41
42 }