Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/modules/mash/screen/main.nf @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 process MASH_SCREEN {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mash${params.fs}2.3" : null)
6 conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
9 'quay.io/biocontainers/mash:2.3--he348c14_1' }"
10
11 input:
12 tuple val(meta), path(query)
13
14 output:
15 tuple val(meta), path("*.screened"), emit: screened
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24 def sequence_sketch = (meta.sequence_sketch ?: '')
25 """
26 mash \\
27 screen \\
28 $args \\
29 -p $task.cpus \\
30 $sequence_sketch \\
31 $query \\
32 > ${prefix}.screened
33
34 cat <<-END_VERSIONS > versions.yml
35 "${task.process}":
36 mash: \$( mash --version )
37 END_VERSIONS
38 """
39 }