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comparison 1.0.0/modules/sourmash/gather/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 SOURMASH_GATHER {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null)
6 conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0':
9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }"
10
11 input:
12 tuple val(meta), path(signature), path(database)
13 val save_unassigned
14 val save_matches_sig
15 val save_prefetch
16 val save_prefetch_csv
17
18 output:
19 tuple val(meta), path("*.csv.gz") , emit: result , optional: true
20 tuple val(meta), path("*_scaffolded_genomic.fna.gz"), emit: genomes_fasta, optional: true
21 tuple val(meta), path("*_unassigned.sig.zip") , emit: unassigned , optional: true
22 tuple val(meta), path("*_matches.sig.zip") , emit: matches , optional: true
23 tuple val(meta), path("*_prefetch.sig.zip") , emit: prefetch , optional: true
24 tuple val(meta), path("*_prefetch.csv.gz") , emit: prefetchcsv , optional: true
25 path "*FAILED.txt" , emit: failed , optional: true
26 path "versions.yml" , emit: versions
27
28 when:
29 task.ext.when == null || task.ext.when
30
31 script:
32 def args = task.ext.args ?: ''
33 def args2 = task.ext.args2 ?: ''
34 def prefix = task.ext.prefix ?: "${meta.id}"
35 def unassigned = save_unassigned ? "--output-unassigned ${prefix}_unassigned.sig.zip" : ''
36 def matches = save_matches_sig ? "--save-matches ${prefix}_matches.sig.zip" : ''
37 def prefetch = save_prefetch ? "--save-prefetch ${prefix}_prefetch.sig.zip" : ''
38 def prefetchcsv = save_prefetch_csv ? "--save-prefetch-csv ${prefix}_prefetch.csv.gz" : ''
39 def gd = params.tuspy_gd ? "-gd ${params.tuspy_gd}" : ''
40
41 """
42 sourmash gather \\
43 $args \\
44 --output ${prefix}.csv.gz \\
45 ${unassigned} \\
46 ${matches} \\
47 ${prefetch} \\
48 ${prefetchcsv} \\
49 ${signature} \\
50 ${database}
51
52 sourmash_filter_hits.py \\
53 $args2 \\
54 -csv ${prefix}.csv.gz
55
56 gen_otf_genome.py \\
57 $gd \\
58 -op ${prefix} \\
59 -txt ${prefix}_template_hits.txt
60
61 cat <<-END_VERSIONS > versions.yml
62 "${task.process}":
63 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' )
64 python: \$( python --version | sed 's/Python //g' )
65 END_VERSIONS
66 """
67 }