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1 process CAT_CAT {
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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}${params.fs}pigz${params.fs}2.7" : null)
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6 conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
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9 'quay.io/biocontainers/pigz:2.3.4' }"
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10
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11 input:
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12 tuple val(meta), path(files_in)
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13
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14 output:
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15 tuple val(meta), path("*${prefix}"), emit: concatenated_reads
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def args2 = task.ext.args2 ?: ''
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24 def file_list = files_in.collect { it.toString() }
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25
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26 // | input | output | command1 | command2 |
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27 // |-----------|------------|----------|----------|
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28 // | gzipped | gzipped | cat | |
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29 // | ungzipped | ungzipped | cat | |
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30 // | gzipped | ungzipped | zcat | |
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31 // | ungzipped | gzipped | cat | pigz |
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32
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33 // Use input file ending as default
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34 prefix = task.ext.prefix ? "${meta.id}.${task.ext.prefix}" : "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
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35 out_zip = prefix.endsWith('.gz')
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36 in_zip = file_list[0].endsWith('.gz')
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37 command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
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38 command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
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39 """
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40 $command1 \\
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41 $args \\
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42 ${file_list.join(' ')} \\
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43 $command2 \\
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44 > ${prefix}
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45
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46 cat <<-END_VERSIONS > versions.yml
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47 "${task.process}":
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48 pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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49 END_VERSIONS
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kkonganti@17
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50 """
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51
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kkonganti@17
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52 stub:
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53 def file_list = files_in.collect { it.toString() }
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54 prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
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kkonganti@17
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55 """
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56 touch $prefix
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57
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58 cat <<-END_VERSIONS > versions.yml
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59 "${task.process}":
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60 pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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61 END_VERSIONS
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62
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63 catver=""
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64 zver=""
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65
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kkonganti@17
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66 if [ "${workflow.containerEngine}" != "null" ]; then
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67 catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
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68 zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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69
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70 else
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71 catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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72 zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
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73 fi
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74
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kkonganti@17
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75 cat <<-END_VERSIONS >> versions.yml
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76 cat: \$catver
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kkonganti@17
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77 zcat: \$zver
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78 END_VERSIONS
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79 """
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80 } |
