Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/modules/shovill/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 SHOVILL {
2 tag "$meta.id"
3 label 'process_low'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}shovill${params.fs}1.1.0" : null)
6 conda (params.enable_conda ? "bioconda::shovill=1.1.0 conda-forge::pigz" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' :
9 'quay.io/biocontainers/shovill:1.1.0--0' }"
10
11 input:
12 tuple val(meta), path(reads)
13
14 output:
15 tuple val(meta), path("${prefix}${params.fs}contigs.fa") , emit: contigs
16 tuple val(meta), path("${prefix}${params.fs}shovill.corrections") , emit: corrections
17 tuple val(meta), path("${prefix}${params.fs}shovill.log") , emit: log
18 tuple val(meta), path("${prefix}${params.fs}{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
19 tuple val(meta), path("${prefix}${params.fs}contigs.{fastg,gfa,LastGraph}") , emit: gfa, optional: true
20 path "versions.yml" , emit: versions
21
22 when:
23 task.ext.when == null || task.ext.when
24
25 script:
26 def args = task.ext.args ?: ''
27 def memory = (task.memory ? task.memory.toGiga() : 16)
28 prefix = (task.ext.prefix ?: meta.id)
29 """
30 shovill \\
31 --R1 ${reads[0]} \\
32 --R2 ${reads[1]} \\
33 $args \\
34 --tmpdir ${prefix}${params.fs}tmp \\
35 --cpus $task.cpus \\
36 --ram $memory \\
37 --outdir $prefix \\
38 --force
39
40 cat <<-END_VERSIONS > versions.yml
41 "${task.process}":
42 shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
43 END_VERSIONS
44 """
45 }