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nextflow.config
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/*
* -------------------------------------------------
* Bidirectional-Flow Nextflow config file
* -------------------------------------------------
* Default config options for all environments.
* Cluster-specific config options should be saved
* in the conf folder and imported under a profile
* name here.
*/
manifest {
homePage = 'https://github.com/rutendos/Bidirectional-Flow'
description = 'The pipeline identifies regions of bidirectional nascent transcription'
mainScript = 'main.nf'
}
// installing dREG from (git clone https://github.com/Danko-Lab/dREG)
// installed rphast from tar ball (install.packages("rphast_1.6.11.tar.gz", repos=NULL, type="source"))
// Global default params, used in configs
params {
version = "0.3" // Pipeline version
// Input arguments
crams = false
bams = false
// Run arguments
workdir = false
genome = false
genome_refseq = false
dreg = false
dreg_results = false
fstitch = false
tfit = false
tfit_prelim = false
tfit_model = false
tfit_split_model = false
prelim_files = false
prelim_process = true
gene_count = false
bidir_count = false
bedtools_count = false
email=false
help = false
outdir = './results'
singleEnd = false
r1_five_prime = false
savestats = true
savebam = false
savetfitbam = false
savebg = false
savebw = false
savebidirs = false
}
profiles {
example {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/example.config'
}
hg38 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/hg38.config'
}
mm10 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/mm10.config'
}
dm6 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/dm6.config'
}
hg38_lysa8537 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/hg38_lysa8537.config'
}
mm10_lysa8537 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/mm10_lysa8537.config'
}
dm6_lysa8537 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/dm6_lysa8537.config'
}
hg38_rusi2317 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/hg38_rusi2317.config'
}
mm10_rusi2317 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/mm10_rusi2317.config'
}
dm6_rusi2317 {
workDir = params.workdir
process.executor = 'slurm'
includeConfig 'conf/dm6_rusi2317.config'
}
}
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/bidir_pipeline_timeline.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/bidir_pipeline_report.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/bidir_pipeline_trace.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/bidir_pipeline_dag.svg"
}