main7.nf

/*
 * Copyright (c) 2013-2019, Centre for Genomic Regulation (CRG).
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * This Source Code Form is "Incompatible With Secondary Licenses", as
 * defined by the Mozilla Public License, v. 2.0.
 *
 */


/*
 * Proof of concept of a RNAseq pipeline implemented with Nextflow
 *
 * Authors:
 * - Paolo Di Tommaso <paolo.ditommaso@gmail.com>
 * - Emilio Palumbo <emiliopalumbo@gmail.com>
 * - Evan Floden <evanfloden@gmail.com>
 */
nextflow.preview.dsl=2 

/*
 * Default pipeline parameters. They can be overriden on the command line eg.
 * given `params.foo` specify on the run command line `--foo some_value`.
 */

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"

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}
 """

include index from './rnaseq-processes' params(params)
include quant from './rnaseq-processes' params(params)
include fastqc from './rnaseq-processes' params(params)
include multiqc from './rnaseq-processes' params(params)

Channel
    .fromFilePairs( params.reads, checkExists: true )
    .set { read_pairs_ch }



workflow {
    index( params.transcriptome )
    
    quant( index.out, read_pairs_ch )
    
    fastqc( read_pairs_ch )
    
    multiqc( 
            quant.out.mix(fastqc.out).collect(),  
            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" )
}