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1 process FASTP {
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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}${params.fs}fastp${params.fs}0.23.2" : null)
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6 conda (params.enable_conda ? "bioconda::fastp=0.23.2 conda-forge::isa-l" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/fastp:0.23.2--h79da9fb_0' :
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9 'quay.io/biocontainers/fastp:0.23.2--h79da9fb_0' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path('*.fastp.fastq.gz') , emit: passed_reads, optional: true
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16 tuple val(meta), path('*.fail.fastq.gz') , emit: failed_reads, optional: true
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17 tuple val(meta), path('*.merged.fastq.gz'), emit: merged_reads, optional: true
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18 tuple val(meta), path('*.json') , emit: json
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19 tuple val(meta), path('*.html') , emit: html
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20 tuple val(meta), path('*.log') , emit: log
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21 path "versions.yml" , emit: versions
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22
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23 when:
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24 task.ext.when == null || task.ext.when
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25
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26 script:
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27 def args = task.ext.args ?: ''
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28 def prefix = task.ext.prefix ?: "${meta.id}"
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29 def fail_fastq = params.fastp_failed_out && meta.single_end ? "--failed_out ${prefix}.fail.fastq.gz" : params.fastp_failed_out && !meta.single_end ? "--unpaired1 ${prefix}_1.fail.fastq.gz --unpaired2 ${prefix}_2.fail.fastq.gz" : ''
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30 // Added soft-links to original fastqs for consistent naming in MultiQC
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31 // Use single ended for interleaved. Add --interleaved_in in config.
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32 if ( task.ext.args?.contains('--interleaved_in') ) {
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33 """
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34 [ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
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35
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36 fastp \\
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37 --stdout \\
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38 --in1 ${prefix}.fastq.gz \\
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39 --thread $task.cpus \\
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40 --json ${prefix}.fastp.json \\
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41 --html ${prefix}.fastp.html \\
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42 $fail_fastq \\
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43 $args \\
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44 2> ${prefix}.fastp.log \\
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45 | gzip -c > ${prefix}.fastp.fastq.gz
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46
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47 cat <<-END_VERSIONS > versions.yml
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48 "${task.process}":
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49 fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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50 END_VERSIONS
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51 """
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52 } else if (meta.single_end) {
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53 """
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54 [ ! -f ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz
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55
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56 fastp \\
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57 --in1 ${prefix}.fastq.gz \\
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58 --out1 ${prefix}.fastp.fastq.gz \\
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59 --thread $task.cpus \\
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60 --json ${prefix}.fastp.json \\
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61 --html ${prefix}.fastp.html \\
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62 $fail_fastq \\
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63 $args \\
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64 2> ${prefix}.fastp.log
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65
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66 cat <<-END_VERSIONS > versions.yml
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67 "${task.process}":
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68 fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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69 END_VERSIONS
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70 """
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71 } else {
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72 def merge_fastq = params.fastp_merged_out ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
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73 """
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74 [ ! -f ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
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75 [ ! -f ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
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76 fastp \\
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77 --in1 ${prefix}_1.fastq.gz \\
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78 --in2 ${prefix}_2.fastq.gz \\
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79 --out1 ${prefix}_1.fastp.fastq.gz \\
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80 --out2 ${prefix}_2.fastp.fastq.gz \\
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81 --json ${prefix}.fastp.json \\
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82 --html ${prefix}.fastp.html \\
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83 $fail_fastq \\
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84 $merge_fastq \\
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85 --thread $task.cpus \\
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86 --detect_adapter_for_pe \\
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87 $args \\
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88 2> ${prefix}.fastp.log
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89
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90 cat <<-END_VERSIONS > versions.yml
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91 "${task.process}":
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92 fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
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93 END_VERSIONS
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94 """
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95 }
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96 } |
