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1 process SAMTOOLS_FASTQ {
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2 tag "$meta.id"
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3 label 'process_micro'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}samtools${params.fs}1.13" : null)
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6 conda (params.enable_conda ? "bioconda::samtools=1.18 bioconda::htslib=1.18 conda-forge::bzip2" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' :
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9 'quay.io/biocontainers/samtools:1.18--h50ea8bc_1' }"
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10
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11 input:
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12 tuple val(meta), path(input)
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13 val(interleave)
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14
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15 output:
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16 tuple val(meta), path("*_{1,2}.fastq.gz") , optional:true, emit: fastq
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17 tuple val(meta), path("*_{1,2}.fastq.gz") , optional:true, emit: mapped_refs
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18 tuple val(meta), path("*_interleaved.fastq") , optional:true, emit: interleaved
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19 tuple val(meta), path("*_singleton.fastq.gz") , optional:true, emit: singleton
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20 tuple val(meta), path("*_other.fastq.gz") , optional:true, emit: other
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21 path "versions.yml" , emit: versions
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22
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23 when:
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24 task.ext.when == null || task.ext.when
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25
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26 script:
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27 def args = task.ext.args ?: ''
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28 def prefix = task.ext.prefix ?: "${meta.id}"
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29 def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq" :
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30 meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
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31 "-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz -s ${prefix}_singleton.fastq.gz"
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32 """
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33 samtools \\
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34 fastq \\
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35 $args \\
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36 --threads ${task.cpus-1} \\
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37 -0 ${prefix}_other.fastq.gz \\
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38 $input \\
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39 $output
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40
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41 samtools \\
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42 view \\
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43 $args2 \\
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44 --threads ${task.cpus-1} \\
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45 $input \\
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46 | grep -v '*' | cut -f3 | sort -u > mapped_refs.txt
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47
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48 cat <<-END_VERSIONS > versions.yml
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49 "${task.process}":
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50 samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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51 END_VERSIONS
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52 """
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53 } |
