Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/modules/flye/assemble/main.nf @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 process FLYE_ASSEMBLE {
2 tag "$meta.id"
3 label 'process_medium'
4 // errorStrategy 'ignore'
5
6 module (params.enable_module ? "${params.swmodulepath}${params.fs}flye${params.fs}2.9" : null)
7 conda (params.enable_conda ? "bioconda::flye=2.9.0" : null)
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
9 'https://depot.galaxyproject.org/singularity/flye:2.9--py38hf4f3596_1' :
10 'quay.io/biocontainers/flye:2.9--py38hf4f3596_1' }"
11
12 input:
13 tuple val(meta), path(reads)
14
15 output:
16 path "${meta.id}${params.fs}*"
17 tuple val(meta), path("${meta.id}${params.fs}assembly.fasta"), emit: assembly, optional: true
18 path "versions.yml" , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 """
26 reads_platform=\$( echo "$args" | grep -E -o '(--nano|--pacbio)-(raw|corr|hq|hifi)' )
27 flye \\
28 \$(echo "$args" | sed -e "s/\$reads_platform//") \\
29 -t $task.cpus \\
30 --out-dir "${meta.id}" \\
31 \$reads_platform \\
32 $reads
33
34 cat <<-END_VERSIONS > versions.yml
35 "${task.process}":
36 flye: \$( flye --version )
37 END_VERSIONS
38
39 grepver=""
40
41 if [ "${workflow.containerEngine}" != "null" ]; then
42 grepver=\$( grep --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
43 else
44 grepver=\$( echo \$( grep --version 2>&1 ) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
45 fi
46
47 cat <<-END_VERSIONS >> versions.yml
48 grep: \$grepver
49 END_VERSIONS
50 """
51 }