RNA-Seq pipeline

This pipeline shows an example of a basic for RNA-Seq analysis that performs quality control, transcript quantification, and result aggregation. The pipeline processes paired-end FASTQ files, generates quality control reports with FastQC, quantifies transcripts with Salmon, and produces a unified report with MultiQC.

// Parameter inputs
params.reads = "${baseDir}/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "${baseDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.outdir = "results"
params.multiqc = "${baseDir}/multiqc"


// Component imports
include { RNASEQ } from './modules/rnaseq'
include { MULTIQC } from './modules/multiqc'


// Workflow block
workflow {

    log.info """\
      R N A S E Q - N F   P I P E L I N E
      ===================================
      transcriptome: ${params.transcriptome}
      reads        : ${params.reads}
      outdir       : ${params.outdir}
    """.stripIndent()

    read_pairs_ch = channel.fromFilePairs(params.reads, checkIfExists: true, flat: true)

    (fastqc_ch, quant_ch) = RNASEQ(read_pairs_ch, params.transcriptome)

    multiqc_files_ch = fastqc_ch.mix(quant_ch).collect()

    MULTIQC(multiqc_files_ch, params.multiqc)

    workflow.onComplete = {
        log.info(
            workflow.success
                ? "\nDone! Open the following report in your browser --> ${params.outdir}/multiqc_report.html\n"
                : "Oops .. something went wrong"
        )
    }
}