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1 process SEQKIT_GREP {
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2 tag "$meta.id"
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3 label 'process_low'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null)
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6 conda (params.enable_conda ? "bioconda::seqkit=2.2.0 conda-forge::sed=4.7 conda-forge::coreutils" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0':
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9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
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10
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11 input:
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12 tuple val(meta), path(reads), path(pattern_file)
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13
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14 output:
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15 tuple val(meta), path("*.gz"), emit: fastx
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}"
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24 def num_read_files = reads.toList().size()
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25 def extension = "fastq"
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26 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) {
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27 extension = "fasta"
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28 }
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29
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30 if (meta.single_end || num_read_files == 1) {
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31 """
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32 pattern_file_contents=\$(sed '1!d' $pattern_file)
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33 if [ "\$pattern_file_contents" != "DuMmY" ]; then
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34 cut -f1 -d " " $pattern_file > ${prefix}.seqids.txt
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35 additional_args="-f ${prefix}.seqids.txt $args"
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36 else
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37 additional_args="$args"
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38 fi
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39
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40 seqkit \\
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41 grep \\
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42 -j $task.cpus \\
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43 -o ${prefix}.seqkit-grep.${extension}.gz \\
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44 \$additional_args \\
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45 $reads
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46
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47 cat <<-END_VERSIONS > versions.yml
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48 "${task.process}":
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49 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
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50 END_VERSIONS
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51 """
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52 } else {
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53 """
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54 pattern_file_contents=\$(sed '1!d' $pattern_file)
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55 if [ "\$pattern_file_contents" != "DuMmY" ]; then
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56 additional_args="-f $pattern_file $args"
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57 else
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58 additional_args="$args"
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59 fi
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60
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61 seqkit \\
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62 grep \\
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63 -j $task.cpus \\
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64 -o ${prefix}.R1.seqkit-grep.${extension}.gz \\
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65 \$additional_args \\
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66 ${reads[0]}
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67
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68 seqkit \\
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69 grep \\
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70 -j $task.cpus \\
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71 -o ${prefix}.R2.seqkit-grep.${extension}.gz \\
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72 \$additional_args \\
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73 ${reads[1]}
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74
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75 seqkit \\
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76 pair \\
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77 -j $task.cpus \\
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78 -1 ${prefix}.R1.seqkit-grep.${extension}.gz \\
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79 -2 ${prefix}.R2.seqkit-grep.${extension}.gz
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80
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81 rm ${prefix}.R1.seqkit-grep.${extension}.gz
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82 rm ${prefix}.R2.seqkit-grep.${extension}.gz
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83
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84 cat <<-END_VERSIONS > versions.yml
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85 "${task.process}":
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86 seqkit: \$( seqkit | sed '3!d; s/Version: //' )
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87 END_VERSIONS
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88 """
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89 }
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90 }
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