Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/medaka/consensus/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 MEDAKA_CONSENSUS {
2 tag "$meta.id"
3 label 'process_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}medaka${params.fs}1.11.2" : null)
6 conda (params.enable_conda ? "bioconda::medaka=1.11.2 conda-forge::python" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/medaka:1.11.2--py310h87e71ce_0' :
9 'quay.io/biocontainers/medaka:1.11.2--py310h87e71ce_0' }"
10
11 input:
12 tuple val(meta), path(bam), path(bai)
13
14 output:
15 tuple val(meta), path("*.hdr"), emit: hdr
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24 """
25 medaka consensus \\
26 --threads $task.cpus \\
27 $args \\
28 $bam \\
29 ${prefix}.medaka.hdr
30
31 cat <<-END_VERSIONS > versions.yml
32 "${task.process}":
33 medaka: \$( medaka --version 2> /dev/null | sed 's/medaka //g' )
34 END_VERSIONS
35 """
36 }