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1 process CENTRIFUGE_CLASSIFY {
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2 tag "$meta.id"
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3 label 'process_medium'
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4
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5 module (params.enable_module ? 'centrifuge' : null)
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6 conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
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9 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path('*.report.txt') , emit: report
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16 tuple val(meta), path('*.output.txt') , emit: output
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17 tuple val(meta), path('*.kreport.txt') , emit: kreport
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18 tuple val(meta), path('*.sam') , optional: true, emit: sam
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19 tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
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20 tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
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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 paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
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30 def db = meta.centrifuge_x ?: ''
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31 def db_name = db.toString().replace(".tar.gz","")
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32 def unaligned = ''
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33 def aligned = ''
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34 if (meta.single_end) {
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35 unaligned = params.centrifuge_save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
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36 aligned = params.centrifuge_save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
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37 } else {
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38 unaligned = params.centrifuge_save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
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39 aligned = params.centrifuge_save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
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40 }
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41 def sam_output = params.centrifuge_out_fmt_sam ? "--out-fmt 'sam'" : ''
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42 """
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43 centrifuge \\
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44 -x $db \\
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45 -p $task.cpus \\
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46 $paired \\
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47 --report-file ${prefix}.centrifuge.report.txt \\
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48 -S ${prefix}.centrifuge.output.txt \\
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49 $unaligned \\
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50 $aligned \\
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51 $sam_output \\
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52 $args
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53
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54 centrifuge-kreport -x $db_name ${prefix}.centrifuge.output.txt > ${prefix}.centrifuge.kreport.txt
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55
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56 cat <<-END_VERSIONS > versions.yml
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57 "${task.process}":
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58 centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
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59 END_VERSIONS
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60 """
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61 } |
