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