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nextflow.config
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nextflow.config
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py3Image = "quay.io/h3abionet_org/py3plink"
gemmaImage="quay.io/h3abionet_org/h3agwas-gemma"
latexImage="quay.io/h3abionet_org/h3agwas-texlive"
swarmPort = '2376'
queue = 'batch'
manifest {
homePage = 'http:/h3abionet/h3agwas'
description = 'GWAS Pipeline for H3Africa'
mainScript = 'plink-qc.nf'
}
aws {
accessKey =''
secretKey =''
region ='eu-west-1'
}
cloud {
imageId = "ami-710b9108" // specify your AMI id here
instanceType = "m4.xlarge"
subnetId = "null"
sharedStorageId = "null"
sharedStorageMount = "/mnt/shared"
bootStorageSize = "20GB" // Size of disk for images spawned
// instanceStorageMount = "" // Set a common mount point for images
// instanceStorageDevice = "" // Set a common block device for images
autoscale {
enabled = true
maxInstances = 1
terminateWhenIdle = true
}
}
params {
// Directories
work_dir = "/$PWD"
input_dir = "${params.work_dir}/input"
output_dir = "${params.work_dir}/output"
scripts = "${params.work_dir}/scripts"
output = "out"
max_forks = 95
// Data
input_pat = "sampleA"
high_ld_regions_fname = ""
sexinfo_available = true
cut_het_high = 0.343
cut_het_low = 0.15
cut_diff_miss = "0.05"
cut_maf = "0.01"
cut_mind = "0.02"
cut_geno = 0.01
cut_hwe = 0.008
pi_hat = 0.11
super_pi_hat = 0.7
f_lo_male = 0.8 // default for F-sex check -- >= means male
f_hi_female = 0.2 // <= means female
case_control = "${params.input_dir}/sample.phe"
case_control_col = "PHE"
phenotype = 0
pheno_col = "all"
batch = 0
batch_col = 0
samplesize = 0 // How many individuals in each genotype report 0=ALL
strandreport =""
manifest = ""
idpat = 0 // or "(\\w+)-DNA_(\\w+)_.*" or ".*_(.*)"
// Needed for topbottom.nf -- uncomment and put in details
// reference = ""
// output_align = ""
// samplesheet = ""
// chipdescription = ""
accessKey = ""
secretKey = ""
region = "eu-west-1"
AMI = "ami-710b9108"
instanceType = "m4.xlarge"
bootStorageSize = "20GB"
maxInstances = "1"
plink_mem_req = "750MB"
other_mem_req = "750MB"
big_time = '12h'
sharedStorageMount = "/mnt/shared"
gemma_num_cores = 8
max_plink_cores = 4
}
profiles {
// For execution on a local machine, no containerization. -- Default
standard {
process.executor = 'local'
}
// For execution on a PBS scheduler, no containerization.
pbs {
process.executor = 'pbs'
process.queue = queue
}
// For execution on a PBS scheduler with containerization.
pbsDocker {
process.executor = 'pbs'
process.container = py3Image
process.executor = 'local'
process.$produceReports.container =latexImage
process.$computeTest.container = "$gemmaImage"
docker.remove = true
docker.runOptions = '--rm'
docker.registry = 'quay.io'
docker.enabled = true
docker.temp = 'auto'
docker.fixOwnership= true
}
// Execute pipeline with Docker locally
docker {
process.executor = 'local'
//process.$produceReports.container =latexImage
//process.$computeTest.container = "$gemmaImage"
//process.$doReport.container =latexImage
docker.remove = true
docker.runOptions = '--rm'
//docker.registry = 'quay.io'
docker.enabled = true
docker.temp = 'auto'
docker.fixOwnership= true
docker.process.executor = 'local'
}
dockerpbs {
process.executor = 'pbs'
process.container = py3Image
process.$produceReports.container ="$latexImage"
process.$computeTest.container = "$gemmaImage"
docker.remove = true
docker.runOptions = '--rm'
docker.registry = 'quay.io'
docker.enabled = true
docker.temp = 'auto'
docker.fixOwnership= true
docker.process.executor = 'local'
docker.fixOwnership = true
}
// Execute pipeline with Docker Swarm setup
dockerSwarm {
process.container = py3Image
process.$produceReports.container ="$latexImage"
process.$computeTest.container = "$gemmaImage"
docker.remove = true
docker.runOptions = '--rm'
docker.registry = 'quay.io'
docker.enabled = true
docker.temp = 'auto'
docker.fixOwnership= true
docker.process.executor = 'local'
docker.engineOptions = "-H :$swarmPort"
}
singularity.cacheDir = "${HOME}/.singularity"
singularity {
singularity.autoMounts = true
singularity.enabled = true
process.executor = 'local'
process.queue = queue
}
singularityPBS {
singularity.autoMounts = true
singularity.enabled = true
process.executor = 'local'
process.queue = queue
}
}
process {
container = py3Image
withLabel:latex {
container = latexImage
}
withLabel: gemma {
container = gemmaImage
}
}
timeline {
enabled=true
file = "nextflow_reports/timeline.html"
}
report {
enabled = true
file = "nextflow_reports/report.html"
}