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comparison 0.2.0/modules/masurca/polish/main.nf @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 process MASURCA_POLISH {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}masurca${params.fs}4.1.0" : null)
6 conda (params.enable_conda ? "bioconda::masurca=4.1.0 conda-forge::libgcc-ng" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/masurca:4.1.0--pl5321hb5bd705_1' :
9 'quay.io/biocontainers/masurca:4.1.0--pl5321hb5bd705_1' }"
10
11 input:
12 tuple val(meta), path(contigs), path(reads)
13
14 output:
15 tuple val(meta), path("${prefix}_contigs.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 memory = (task.memory ? task.memory.toGiga() : 16)
24 def mem_per_thread = memory.toGiga().toInteger().div(task.cpus.toInteger()).round(0)
25 def all_reads = "${reads.join(' ')}"
26 prefix = (task.ext.prefix ?: meta.id)
27 """
28 polca.sh \\
29 -a $contigs \\
30 -r '${all_reads}' \\
31 -t $task.cpus \\
32 -m $mem_per_thread \\
33 $args \\
34
35 mv 'contigs.fa' "${prefix}.contigs.fa"
36
37 cat <<-END_VERSIONS > versions.yml
38 "${task.process}":
39 masurca: \$(echo \$(masurca --version 2>&1) | sed 's/^.*version //')
40 END_VERSIONS
41 """
42 }