Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/polypolish/main.nf @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process POLYPOLISH {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}polypolish${params.fs}0.5.0" : null)
6 conda (params.enable_conda ? "bioconda::polypolish=0.5.0 conda-forge::libgcc-ng" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/polypolish:0.5.0--hdbdd923_4' :
9 'quay.io/biocontainers/polypolish:0.5.0--hdbdd923_4' }"
10
11 input:
12 tuple val(meta), path(genome), path(sam)
13
14 output:
15 tuple val(meta), path("*.polished.fa"), emit: polished
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24 """
25
26 polypolish \\
27 $args \\
28 $genome \\
29 ${sam.join(' ')} > ${prefix}.polished.fa
30
31 cat <<-END_VERSIONS > versions.yml
32 "${task.process}":
33 polypolish: \$(echo \$(polypolish -V 2>&1) | sed 's/^Polypolish v//')
34 END_VERSIONS
35 """
36 }