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1 process FASTQC {
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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}${params.fs}fastqc${params.fs}0.11.9" : null)
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6 conda (params.enable_conda ? "conda-forge::perl bioconda::fastqc=0.11.9" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
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9 'quay.io/biocontainers/fastqc:0.11.9--0' }"
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10
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11 input:
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12 tuple val(meta), path(reads)
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13
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14 output:
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15 tuple val(meta), path("*.html"), emit: html
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16 tuple val(meta), path("*.zip") , emit: zip
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17 path "versions.yml" , emit: versions
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18
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19 when:
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20 task.ext.when == null || task.ext.when
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21
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22 script:
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23 def args = task.ext.args ?: ''
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24 // Add soft-links to original FastQs for consistent naming in pipeline
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25 def prefix = task.ext.prefix ?: "${meta.id}"
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26 if (meta.single_end) {
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27 """
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28 [ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
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29 fastqc $args --threads $task.cpus ${prefix}.fastq.gz
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30
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31 cat <<-END_VERSIONS > versions.yml
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32 "${task.process}":
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33 fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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34 END_VERSIONS
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35 """
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36 } else {
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37 """
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38 [ ! -f ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
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39 [ ! -f ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
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40 fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
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41
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42 cat <<-END_VERSIONS > versions.yml
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43 "${task.process}":
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44 fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
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45 END_VERSIONS
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46 """
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47 }
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48 } |
