main.nf

params.reads = "$baseDir/data/ggal/gut_{1,2}.fq"
params.multiqc = "$baseDir/multiqc"
params.outdir = "output"

log.info "~~~ Nextflow Bioinformatics Basic Pipeline ~~"
log.info "* reads:              ${params.reads}"
log.info "* outdir:             ${params.outdir}"
log.info "* Launch dir:         ${workflow.launchDir}"
log.info "* Work dir:           ${workflow.workDir}"
log.info "* Profile             ${workflow.profile ?: '-'}"
log.info "* Workflow container  ${workflow.container ?: '-'}"
log.info "* container engine    ${workflow.containerEngine?:'-'}"
log.info "* Nextflow run name   ${workflow.runName}"


Channel.fromFilePairs( params.reads )
        .ifEmpty { error "Cannot find any reads matching: ${params.reads}"  }
        .into { read_pairs_ch; read_pairs2_ch }


process fastqc {
    tag "${sample_id}"

    input:
    set sample_id, file(reads) from read_pairs2_ch

    output:
    file("fastqc_${sample_id}_logs") into fastqc_ch


    script:
    """
    mkdir fastqc_${sample_id}_logs
    fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
    """
}


process multiqc {
    publishDir params.outdir, mode:'copy'

    input:
    file('*') from fastqc_ch.collect()

    output:
    file('multiqc_report.html')

    script:
    """
    multiqc .
    """
}


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