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kkonganti@92
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1 process KRAKEN2_CLASSIFY {
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kkonganti@92
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2 tag "$meta.id"
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kkonganti@92
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3 label 'process_low'
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kkonganti@92
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4
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kkonganti@92
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}kraken2${params.fs}2.1.2" : null)
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kkonganti@92
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6 conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null)
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kkonganti@92
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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kkonganti@92
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8 'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
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kkonganti@92
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9 'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
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kkonganti@92
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10
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kkonganti@92
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11 input:
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kkonganti@92
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12 tuple val(meta), path(reads)
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kkonganti@92
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13
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kkonganti@92
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14 output:
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kkonganti@92
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15 tuple val(meta), path('*classified*') , emit: classified
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kkonganti@92
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16 tuple val(meta), path('*unclassified*'), emit: unclassified
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kkonganti@92
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17 tuple val(meta), path('*.report.txt') , emit: kraken_report
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kkonganti@92
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18 tuple val(meta), path('*.output.txt') , emit: kraken_output
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kkonganti@92
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19 path "versions.yml" , emit: versions
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kkonganti@92
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20
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kkonganti@92
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21 when:
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kkonganti@92
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22 task.ext.when == null || task.ext.when || reads
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kkonganti@92
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23
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kkonganti@92
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24 script:
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kkonganti@92
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25 def args = task.ext.args ?: ''
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kkonganti@92
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26 def db = meta.kraken2_db ?: ''
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kkonganti@92
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27 def prefix = task.ext.prefix ?: "${meta.id}"
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kkonganti@92
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28 def readList = reads.collect{ it.toString() }
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kkonganti@92
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29 def is_single_end = (meta.single_end || meta.is_assembly) ? true : false
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kkonganti@92
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30 def paired = is_single_end ? "" : "--paired"
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kkonganti@92
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31 def classified = is_single_end ? "--classified-out ${prefix}.classified.fastq" : "--classified-out ${prefix}.classified#.fastq"
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kkonganti@92
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32 def unclassified = is_single_end ? "--unclassified-out ${prefix}.unclassified.fastq" : "--unclassified-out ${prefix}.unclassified#.fastq"
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kkonganti@92
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33 args += (reads.getName().endsWith(".gz") ? ' --gzip-compressed ' : '')
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kkonganti@92
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34 """
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kkonganti@92
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35 kraken2 \\
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kkonganti@92
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36 --db $db \\
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kkonganti@92
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37 --threads $task.cpus \\
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kkonganti@92
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38 $unclassified \\
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kkonganti@92
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39 $classified \\
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kkonganti@92
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40 --report ${prefix}.kraken2.report.txt \\
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kkonganti@92
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41 --output ${prefix}.kraken2.output.txt \\
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kkonganti@92
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42 $paired \\
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kkonganti@92
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43 $args \\
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kkonganti@92
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44 $reads
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kkonganti@92
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45
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kkonganti@92
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46 cat <<-END_VERSIONS > versions.yml
|
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kkonganti@92
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47 "${task.process}":
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kkonganti@92
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48 kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
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kkonganti@92
|
49 END_VERSIONS
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kkonganti@92
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50
|
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kkonganti@92
|
51 zcmd=""
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kkonganti@92
|
52 zver=""
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|
kkonganti@92
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53
|
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kkonganti@92
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54 if type pigz > /dev/null 2>&1; then
|
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kkonganti@92
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55 pigz -p $task.cpus *.fastq
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kkonganti@92
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56 zcmd="pigz"
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kkonganti@92
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57 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
|
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kkonganti@92
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58 elif type gzip > /dev/null 2>&1; then
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kkonganti@92
|
59 gzip *.fastq
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kkonganti@92
|
60 zcmd="gzip"
|
|
kkonganti@92
|
61
|
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kkonganti@92
|
62 if [ "${workflow.containerEngine}" != "null" ]; then
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kkonganti@92
|
63 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
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|
kkonganti@92
|
64 else
|
|
kkonganti@92
|
65 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
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|
kkonganti@92
|
66 fi
|
|
kkonganti@92
|
67 fi
|
|
kkonganti@92
|
68
|
|
kkonganti@92
|
69 cat <<-END_VERSIONS >> versions.yml
|
|
kkonganti@92
|
70 \$zcmd: \$zver
|
|
kkonganti@92
|
71 END_VERSIONS
|
|
kkonganti@92
|
72 """
|
|
kkonganti@92
|
73 } |
