nextflow.config

//
// There should be no need to change this
//

nextflowVersion = '>=20.10.0'
singularity.autoMounts = true
singularity.enabled = true
trace.enabled = true
report.enabled = true
dag.enabled = true

//
// You may need to change this, based on your computing environment
//

// If you use a workload manager besides SLURM, you can replace 'slurm' with the relevant workload manager, if supported: https://www.nextflow.io/docs/latest/executor.html
// If you don't use a supported workload manager, you can replace 'slurm' with 'local'
process {
    executor='slurm'
    shell = ['/bin/bash', '-ueo', 'pipefail']
}

// if the executor above is set to 'local' (i.e. you aren't using a supported workload manager),
// specify the computing resources available for running commands on your machine here
executor {
    name = 'local'
    cpus = 5
    memory = '300 GB'
}

//
// Below are the key file names you'll need to change
//

params.blacklist = ['hg19': ['/lab/data/reference/human/hg19/annot/wgEncodeDacMapabilityConsensusExcludable.bed.gz', '/lab/data/reference/human/hg19/annot/wgEncodeDukeMapabilityRegionsExcludable.bed.gz'], 'mm9': ['/lab/data/reference/mouse/mm9/annot/mm9-blacklist.bed.gz'], 'rn6': ['/lab/work/porchard/data/mappability.new/rn6.blacklist.1.bed.gz'], 'mm10': ['/lab/work/porchard/reference/mappability/mm10/mm10-blacklist.v2.bed.gz']]
params.chrom_sizes = ['hg19': '/lab/data/reference/human/hg19/hg19.chrom_sizes', 'rn6': '/lab/work/porchard/data/chrom_sizes/rn6.chrom_sizes', 'rn7': '/lab/data/reference/rat/rn7/annot/rn7.chrom.sizes', 'mm10': '/lab/work/porchard/reference/chrom-sizes/mm10.chrom_sizes']
params.bwa_index = ['hg19': '/lab/work/porchard/data/bwa/hg19/hg19', 'rn6': '/lab/work/porchard/data/bwa/rn6/rn6', 'rn7': '/lab/work/porchard/data/bwa/rn7/rn7', 'mm10': '/lab/work/porchard/reference/bwa/0.7.15/mm10/mm10']
params.tss = ['hg19': '/home/porchard/github/ataqv/data/tss/hg19.tss.refseq.bed.gz', 'rn6': '/home/porchard/github/ataqv/data/tss/rn6.tss.refseq.bed.gz', 'rn7':'/home/porchard/github/ataqv/data/tss/rn7.tss.refseq.bed.gz', 'mm10': '/lab/work/porchard/reference/tss/mm10.gencode.tss.bed.gz']
params.plot_signal_at_genes = ['GAPDH']