Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/top_unique_serovars/main.nf @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 process TOP_UNIQUE_SEROVARS {
2 tag "$meta.id"
3 label "process_pico"
4 maxForks 5
5
6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
7 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
9 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
10 'quay.io/biocontainers/python:3.10.4' }"
11
12 input:
13 tuple val(meta), path(mash_screen_res)
14
15 output:
16 tuple val(meta), path('*_UNIQUE_HITS.txt') , emit: tsv, optional: true
17 tuple val(meta), path('*_UNIQUE_HITS_POPUP.txt'), emit: popup, optional: true
18 tuple val(meta), path('*_UNIQUE_HITS_ACCS.txt') , emit: accessions, optional: true
19 tuple val(meta), path('*_UNIQUE_HITS.fna.gz') , emit: genomes_fasta, optional: true
20 path'*FAILED.txt' , emit: failed, optional: true
21 path 'versions.yml' , emit: versions
22
23 when:
24 task.ext.when == null || task.ext.when
25
26 script:
27 def args = task.ext.args ?: ''
28 def prefix = task.ext.prefix ?: "${meta.id}"
29 args += (mash_screen_res ? " -m ${mash_screen_res}" : '')
30 args += (prefix ? " -op ${prefix}" : '')
31 """
32 get_top_unique_mash_hit_genomes.py \\
33 $args
34
35 cat <<-END_VERSIONS > versions.yml
36 "${task.process}":
37 python: \$( python --version | sed 's/Python //g' )
38 datasets: \$( datasets --version | sed 's/datasets version: //g' )
39 dataformat: \$( dataformat version )
40 END_VERSIONS
41 """
42
43 }