Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/megahit/assemble/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 MEGAHIT_ASSEMBLE {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}megahit${params.fs}1.2.9" : null)
6 conda (params.enable_conda ? "conda-forge::python bioconda::megahit=1.2.9" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/megahit:1.2.9--h2e03b76_1' :
9 'quay.io/biocontainers/megahit:1.2.9--h2e03b76_1' }"
10
11 input:
12 tuple val(meta), path(reads)
13
14 output:
15 tuple val(meta), path("${meta.id}${params.fs}${meta.id}.contigs.fa"), emit: assembly, optional: true
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 maxmem = task.memory ? "--memory ${task.memory.toBytes()}" : ""
25 if (meta.single_end) {
26 """
27 megahit \\
28 -r ${reads} \\
29 -t $task.cpus \\
30 $maxmem \\
31 $args \\
32 --out-dir $prefix \\
33 --out-prefix $prefix
34
35 cat <<-END_VERSIONS > versions.yml
36 "${task.process}":
37 megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
38 END_VERSIONS
39 """
40 } else {
41 """
42 megahit \\
43 -1 ${reads[0]} \\
44 -2 ${reads[1]} \\
45 -t $task.cpus \\
46 $maxmem \\
47 $args \\
48 --out-dir $prefix \\
49 --out-prefix $prefix
50
51 cat <<-END_VERSIONS > versions.yml
52 "${task.process}":
53 megahit: \$(echo \$(megahit -v 2>&1) | sed 's/MEGAHIT v//')
54 END_VERSIONS
55 """
56 }
57 }