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