main.nf

#!/usr/bin/env nextflow 

/*
 * Proof of concept of a RNAseq pipeline implemented with Nextflow
 */


/*
 * 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"


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

/* 
 * main script flow
 */
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}
  """

  read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true ) 
  RNASEQ( params.transcriptome, read_pairs_ch )
  MULTIQC( RNASEQ.out, params.multiqc )
}