Nextflow
Workflow managers
The Makefile has been getting a little scary. It's great for one off commands
for a project, but not so much for full blown data pipelines. There are plenty
of more modern alternatives.
What is Nextflow?
Nextflow is an incredibly powerful and flexible workflow language. It's mainly used for bioinformatics analysis.
main.nf
/*
* 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 = "$baseDir/data/ggal/*_{1,2}.fq"
params.transcriptome = "$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}
"""
// import modules
include { RNASEQ } from './modules/rnaseq'
include { MULTIQC } from './modules/multiqc'
/*
* main script flow
*/
workflow {
read_pairs_ch = channel.fromFilePairs( params.reads, checkIfExists: true )
RNASEQ( params.transcriptome, read_pairs_ch )
MULTIQC( RNASEQ.out, params.multiqc )
}
/*
* completion handler
*/
workflow.onComplete {
log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
}
The thing that sets Nextflow apart is that it pushes the data through the pipeline, rather than pulling it through like make.
Subworkflows
./modules/rnaseq.nf
params.outdir = 'results'
include { INDEX } from './index'
include { QUANT } from './quant'
include { FASTQC } from './fastqc'
workflow RNASEQ {
take:
transcriptome
read_pairs_ch
main:
INDEX(transcriptome)
FASTQC(read_pairs_ch)
QUANT(INDEX.out, read_pairs_ch)
emit:
QUANT.out | concat(FASTQC.out) | collect
}
Modules
./modules/index.nf
process INDEX {
tag "$transcriptome.simpleName"
input:
path transcriptome
output:
path 'index'
script:
"""
salmon index --threads $task.cpus -t $transcriptome -i index
"""
}