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main3.nf
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main3.nf
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/*
* 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 <[email protected]>
* - Emilio Palumbo <[email protected]>
* - Evan Floden <[email protected]>
*/
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 : ${params.outdir}
"""
Channel
.fromFilePairs( params.reads, checkExists:true )
.set{ read_pairs_ch }
process index {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}
process quant {
tag "$pair_id"
input:
path index
tuple pair_id, path(reads)
output:
path pair_id
script:
"""
salmon quant --threads $task.cpus --libType=U -i $index -1 ${reads[0]} -2 ${reads[1]} -o $pair_id
"""
}
process fastqc {
tag "FASTQC on $sample_id"
publishDir params.outdir
input:
tuple sample_id, path(reads)
output:
path "fastqc_${sample_id}_logs"
script:
"""
mkdir fastqc_${sample_id}_logs
fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}
"""
}
process multiqc {
publishDir params.outdir, mode:'copy'
input:
path 'data*/*'
path config
output:
path 'multiqc_report.html'
script:
"""
cp $config/* .
echo "custom_logo: \$PWD/logo.png" >> multiqc_config.yaml
multiqc -v .
"""
}
workflow {
index(params.transcriptome)
}
workflow.onComplete {
log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
}