rna-seq.nf

#!/usr/bin/env nextflow

// Define input variables
params.deriva = "${baseDir}/../test_data/deriva-cookies.txt"
params.bdbag = "${baseDir}/../test_data/Study_Q-Y4H0.zip"

params.outDir = "${baseDir}/../output"

// Parse input variables
deriva = Channel
  .fromPath(params.deriva)
  .ifEmpty { exit 1, "deriva cookie file not found: ${params.deriva}" }
bdbag = Channel
  .fromPath(params.bdbag)
  .ifEmpty { exit 1, "bdbag zip file not found: ${params.bdbag}" }

outDir = params.outDir

/*
 * splitData: split bdbag files by replicate so fetch can occure in parallel
 */
process splitData {
    tag "${bdbag.baseName}"
    publishDir "${outDir}/temp/${task.process}", mode: "symlink"

    input:
        file bdbag

    output:
        file("Replicate_*.zip") into bdbagSplit mode flatten
        file("${bdbag.baseName}/data/File.csv") into fileMeta
        file("${bdbag.baseName}/data/Experiment Settings.csv") into experimentSettingsMeta
        file("${bdbag.baseName}/data/Experiment.csv") into experimentMeta

    script:
        """
        hostname
        ulimit -a
        study=\$(echo "${bdbag}" | cut -d'.' -f1)
        echo LOG: \${study}
        unzip ${bdbag}
        echo LOG: bdgag unzipped
        python3 ${baseDir}/scripts/modifyFetch.py --fetchFile \${study}
        echo LOG: fetch file filtered for only .fastq.gz
        python3 ${baseDir}/scripts/splitFetch.py --fetchFile \${study}
        echo LOG: fetch file split by replicates
        sh ${baseDir}/scripts/splitBag.sh \${study}
        echo LOG: bag recreated with replicate split fetch file
        """
}

/*
 * getData: fetch study files from consortium with downloaded bdbag.zip
 */
process getData {
    tag "${rep.baseName}"
    publishDir "${outDir}/temp/${task.process}", mode: "symlink"

    input:
        file deriva
        each rep from bdbagSplit

    output:
        file("**/*.R*.fastq.gz") into fastq

    script:
        """
        hostname
        ulimit -a
        replicate=\$(echo "${rep}" | cut -d'.' -f1)
        echo LOG: \${replicate}
        cp "${deriva}" ~/.bdbag/deriva-cookies.txt
        echo LOG: deriva cookie loaded
        unzip ${rep}
        echo LOG: replicate bdbag unzipped
        sh ${baseDir}/scripts/bdbagFetch.sh \${replicate}
        echo LOG: replicate bdbag fetched
        sh ${baseDir}/scripts/renameFastq.sh \${replicate}
        echo LOG: fastq.gz files renamed to replicate RID
        """
 }