Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/filtlong/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 FILTLONG {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}filtlong${params.fs}0.2.1" : null)
6 conda (params.enable_conda ? "conda-forge::gcc bioconda::filtlong=0.2.1" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
9 'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
10
11 input:
12 tuple val(meta), path(shortreads), path(longreads)
13
14 output:
15 tuple val(meta), path("*.filtlong.fastq.gz"), emit: filtered_reads
16 tuple val(meta), path("*.filtlong.log") , emit: log
17 path "versions.yml" , emit: versions
18
19 when:
20 task.ext.when == null || task.ext.when
21
22 script:
23 def args = task.ext.args ?: ''
24 def prefix = task.ext.prefix ?: "${meta.id}"
25 def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
26 if ("$longreads" == "${prefix}.filtlong.fastq.gz") error "Longread FASTQ input and output names are the same, set prefix in module configuration to disambiguate!"
27 """
28 filtlong \\
29 $short_reads \\
30 $args \\
31 $longreads \\
32 2> >(tee ${prefix}.filtlong.log >&2) \\
33 | gzip -n > ${prefix}.filtlong.fastq.gz
34
35 cat <<-END_VERSIONS > versions.yml
36 "${task.process}":
37 filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" )
38 END_VERSIONS
39 """
40 }