main.nf

#!/usr/bin/env nextflow

/*
vim: syntax=groovy
-*- mode: groovy;-*-
========================================================================================
                                     Example Pipeline
========================================================================================
 Example pipeline. Started December 2016.
 @Authors
 Rickard Hammarén <rickard.hammaren@scilifelab.se>
----------------------------------------------------------------------------------------
 Basic command:
 $ nextflow main.nf

 Pipeline variables can be configured with the following command line options:
 --genome [GRCh37 | GRCm38]
 --index [path to STAR index]
 --gtf [path to GTF file]
 --files [path to input files]

----------------------------------------------------------------------------------------
*/
/*
 * SET UP CONFIGURATION VARIABLES
 */

// Pipeline version
version = 0.1

// Reference genome index
params.genome = false
params.gtf   = params.genomes[ params.genome ].gtf
params.bowtie2 = params.genomes[ params.genome ].bowtie2
params.name = "miRNA-Seq Best practice"

// Input files
params.input = "data/*.fastq.gz"

// Output path
params.out = "$PWD"

// R library locations
params.rlocation = "$HOME/R/nxtflow_libs/"
nxtflow_libs=file(params.rlocation)

log.info "===================================="
log.info " Example Pipeline v${version}"
log.info "===================================="
log.info "Reads        : ${params.input}"
log.info "Genome       : ${params.genome}"
log.info "Index        : ${params.bowtie2}"
log.info "Annotation   : ${params.gtf}"
log.info "Current home : $HOME"
log.info "Current user : $USER"
log.info "Current path : $PWD"
log.info "R libraries  : ${params.rlocation}"
log.info "Script dir   : $baseDir"
log.info "Working dir  : $workDir"
log.info "Output dir   : ${params.out}"
log.info "===================================="


/*
 * Create a channel for input read files
 */
Channel
    .fromFilePairs( params.reads, size: -1 )
    .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}" }
    .into { read_files_fastqc; read_files_trimming }

process fastqc {
    tag "$name"
    publishDir "${params.outdir}/fastqc", mode: 'copy'

    input:
    set val(name), file(reads) from read_files_fastqc

    output:
    file "*_fastqc.{zip,html}" into fastqc_results

    script:
    """
    fastqc -q $reads
    """
}