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1 process CAT_FASTQ {
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2 tag "$meta.id"
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3 label 'process_micro'
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4
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5 conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::gzip" : null)
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6 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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7 'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
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8 'biocontainers/biocontainers:v1.2.0_cv1' }"
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9
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10 input:
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11 tuple val(meta), path(reads, stageAs: "input*/*")
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12
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13 output:
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14 tuple val(meta), path("*.merged.fastq.gz"), emit: catted_reads
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15 path "versions.yml" , emit: versions
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16
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17 when:
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18 task.ext.when == null || task.ext.when
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19
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20 script:
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21 def args = task.ext.args ?: ''
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22 def prefix = task.ext.prefix ?: "${meta.id}"
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23 def readList = reads.collect{ it.toString() }
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24 def is_in_gz = readList[0].endsWith('.gz')
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25 def gz_or_ungz = (is_in_gz ? '' : ' | gzip')
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26 def pigz_or_ungz = (is_in_gz ? '' : " | pigz -p ${task.cpus}")
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27 if (meta.single_end) {
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28 if (readList.size > 1) {
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29 """
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30 zcmd="gzip"
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31 zver=""
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32
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33 if type pigz > /dev/null 2>&1; then
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34 cat ${readList.join(' ')} ${pigz_or_ungz} > ${prefix}.merged.fastq.gz
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35 zcmd="pigz"
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36 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
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37 else
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38 cat ${readList.join(' ')} ${gz_or_ungz} > ${prefix}.merged.fastq.gz
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39 zcmd="gzip"
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40
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41 if [ "${workflow.containerEngine}" != "null" ]; then
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42 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
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43 else
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44 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
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45 fi
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46 fi
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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 cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
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51 \$zcmd: \$zver
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52 END_VERSIONS
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53 """
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54 }
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55 } else {
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56 if (readList.size > 2) {
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57 def read1 = []
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58 def read2 = []
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59 readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
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60 """
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61 zcmd="gzip"
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62 zver=""
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63
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64 if type pigz > /dev/null 2>&1; then
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65 cat ${read1.join(' ')} ${pigz_or_ungz} > ${prefix}_1.merged.fastq.gz
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66 cat ${read2.join(' ')} ${pigz_or_ungz} > ${prefix}_2.merged.fastq.gz
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67 zcmd="pigz"
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68 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
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69 else
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70 cat ${read1.join(' ')} ${gz_or_ungz} > ${prefix}_1.merged.fastq.gz
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71 cat ${read2.join(' ')} ${gz_or_ungz} > ${prefix}_2.merged.fastq.gz
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72 zcmd="gzip"
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73
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74 if [ "${workflow.containerEngine}" != "null" ]; then
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75 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
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76 else
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77 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
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78 fi
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79 fi
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80
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81 cat <<-END_VERSIONS > versions.yml
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82 "${task.process}":
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83 cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
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84 \$zcmd: \$zver
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85 END_VERSIONS
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86 """
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87 }
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88 }
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89 } |
