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comparison 1.0.0/modules/minimap2/align/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 MINIMAP2_ALIGN {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ?
6 "${params.swmodulepath}${params.fs}minimap2${params.fs}2.22:${params.swmodulepath}${params.fs}samtools${params.fs}1.13" : null)
7 conda (params.enable_conda ? "bioconda::minimap2=2.24 bioconda::samtools=1.18 conda-forge::perl" : null)
8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
9 'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:365b17b986c1a60c1b82c6066a9345f38317b763-0' :
10 'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:365b17b986c1a60c1b82c6066a9345f38317b763-0' }"
11
12 input:
13 tuple val(meta), path(reads)
14 tuple val(meta2), path(reference)
15 val bam_format
16 val align_bam_sorted
17 val cigar_paf_format
18 val cigar_bam
19
20 output:
21 tuple val(meta), path("*.paf"), emit: paf, optional: true
22 tuple val(meta), path("*.bam"), emit: bam, optional: true
23 tuple val(meta), path("*.bai"), emit: bai, optional: true
24 path "versions.yml" , emit: versions
25
26 when:
27 task.ext.when == null || task.ext.when
28
29 script:
30 def args = task.ext.args ?: ''
31 def prefix = task.ext.prefix ?: "${meta.id}"
32 def bam_sort = align_bam_sorted ? "samtools sort | samtools view -@${task.cpus} -b -h -o ${prefix}.bam; samtools index -@${task.cpus} ${prefix}.bam" : "samtools view -@${task.cpus} -b -h -o ${prefix}.bam"
33 def bam_output = bam_format ? "-a | ${bam_sort}" : "-o ${prefix}.paf"
34 def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
35 def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
36 """
37 minimap2 \\
38 $args \\
39 -t $task.cpus \\
40 "${reference ?: reads}" \\
41 "$reads" \\
42 $cigar_paf \\
43 $set_cigar_bam \\
44 $bam_output
45
46 cat <<-END_VERSIONS > versions.yml
47 "${task.process}":
48 minimap2: \$(minimap2 --version 2>&1)
49 samtools: \$(samtools version | head -n1 | sed -e 's/samtools //' 2>&1)
50 END_VERSIONS
51 """
52 }