Nextflow Configuration
Nextflow pipelines look for a configuration file nextflow.config at runtime to determine resource allocation and
define any environment variables required for any process. The longitudinal GWAS pipeline
provides a default configuration file for users to manage resource allocation and define environment
variables specifying the paths of the outputs and cache directory. Users can use the -C <config-file> option to use a custom configuration file and override the default longGWAS configuration. In addition, the default longGWAS config file supports the use of cloud-based executors such as the Google Cloud batch (gcb) profile. To read more about Nextflow profiles please refer to the Nextflow documentation.
By default, each task is launched using the standard profile. The process labels
small, medium, and large_mem are used to manage resource allocation between 3 types of tasks within the pipeline. small tasks run in parallel, each with access to 2 CPUs and 6GB of working memory. This label is typically assigned to
the model fitting jobs. medium and large_mem tasks have access to 4 CPUs with 12GB of working memory each. These tasks benefit
from access to multiple cores and are typically run consecutively to take advantage of the full capacity of the
compute resources. When running on cloud-based profiles, such as adwb or biowulf, the medium and large_mem tasks will have access to more CPUs and RAM to take full advantage of the increased resources.
Below is the default nextflow.config file used by the longitudinal GWAS pipeline, which includes the default longGWAS parameters (which can be customised using Command line parameters) and profile specifications:
params {
input = "$PWD/example/genotype/chr[1-3].vcf"
covarfile = "$PWD/example/covariates.tsv"
phenofile = "$PWD/example/phenotype.cs.tsv"
//Variables names
pheno_name = 'y'
covariates = 'SEX age_at_baseline'
study_col = 'study_arm'
time_col = 'study_days'
// Model variables
longitudinal_flag = false
survival_flag = false
linear_flag = true
chunk_flag = true
chunk_size = 30000
plink_chunk_size = 10000
//# Parameters for genetic QC
r2thres = -9
minor_allele_freq = '0.05'
minor_allele_ct = '20'
kinship = '0.177'
ancestry = 'EUR'
assembly = 'hg19'
//#Identifier for the input genotype files - useful to cache results
dataset = 'TEST'
//# Generate manhattan with result files
mh_plot = true
}
// Create profiles
profiles {
standard {
env {
RESOURCE_DIR = "$PWD/files"
OUTPUT_DIR = "$PWD/files/longGWAS_pipeline/results"
STORE_DIR = "$PWD/files/longGWAS_pipeline/results/cache"
ADDI_QC_PIPELINE = '/usr/src/ADDI-GWAS-QC-pipeline/addi_qc_pipeline.py'
}
process {
container = 'amcalejandro/longgwas:v2'
cpus = 2
withLabel: small {
cpus = 2
memory = '6 GB'
}
withLabel: medium {
cpus = 4
memory = '12 GB'
}
withLabel: large_mem {
cpus = 4
memory = '12 GB'
}
}
docker {
enabled = true
temp = 'auto'
}
}
adwb {
env {
RESOURCE_DIR = '/files'
OUTPUT_DIR = '/files/longGWAS_pipeline/results'
STORE_DIR = '/files/longGWAS_pipeline/cache'
ADDI_QC_PIPELINE = '/usr/src/ADDI-GWAS-QC-pipeline/addi_qc_pipeline.py'
}
process {
container = 'gwas-pipeline'
cpus = 2
withLabel: small {
cpus = 2
memory = '5 GB'
}
withLabel: medium {
cpus = 2
memory = '15 GB'
}
withLabel: large_mem {
cpus = 10
memory = '70 GB'
}
}
executor {
cpus = 20
name = 'local'
memory = '75 GB'
}
docker {
enabled = true
temp = 'auto'
}
}
biowulf {
env {
RESOURCE_DIR = '/files'
OUTPUT_DIR = "$LONG_GWAS_DIR/$PROJECT_NAME/results"
STORE_DIR = "$LONG_GWAS_DIR/Data/Cache"
ADDI_QC_PIPELINE = '/usr/src/ADDI-GWAS-QC-pipeline/addi_qc_pipeline.py'
}
process {
container = "$LONG_GWAS_DIR/Docker/gwas-pipeline_survival.sif"
cpus = 2
withLabel: small {
cpus = 2
memory = '5 GB'
}
withLabel: medium {
cpus = 2
memory = '15 GB'
}
withLabel: large_mem {
cpus = 10
memory = '115 GB'
}
}
executor {
cpus = 20
name = 'local'
memory = '125 GB'
}
singularity {
enabled = true
temp = 'auto'
runOptions = "--bind $PWD --env APPEND_PATH=$PWD/bin"
}
}
gls {
env {
RESOURCE_DIR = 'gs://long-gwas/nextflow-test/files'
OUTPUT_DIR = 'gs://long-gwas/nextflow-test/files/results'
STORE_DIR = 'gs://long-gwas/nextflow-test/files/cache'
ADDI_QC_PIPELINE = '/usr/src/ADDI-GWAS-QC-pipeline/addi_qc_pipeline.py'
}
process {
cpus = 4
withLabel: small {
cpus = 4
memory = '12 GB'
}
withLabel: medium {
cpus = 4
memory = '12 GB'
}
withLabel: large_mem {
cpus = 4
memory = '12 GB'
}
}
workDir = 'gs://long-gwas/nextflow-test/workdir'
process.executor = 'google-lifesciences'
process.container = 'amcalejandro/longgwas:v2'
google.location = 'us-central1'
google.project = 'gp2-data-explorer'
google.region = 'us-central1'
google.lifeSciences.bootDiskSize = '20GB'
process.cpus = 8
process.memory = '32 GB'
process.disk = '30 GB'
errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
}
gcb {
env {
RESOURCE_DIR = 'gs://long-gwas/nextflow-test-batch/files'
OUTPUT_DIR = 'gs://long-gwas/nextflow-test-batch/files/results'
STORE_DIR = 'gs://long-gwas/nextflow-test-batch/files/cache'
ADDI_QC_PIPELINE = '/usr/src/ADDI-GWAS-QC-pipeline/addi_qc_pipeline.py'
}
process {
container = 'amcalejandro/longgwas:v2'
cpus = 2
withLabel: small {
cpus = 2
memory = '6 GB'
}
withLabel: medium {
cpus = 2
memory = '6 GB'
}
withLabel: large_mem {
cpus = 2
memory = '6 GB'
}
}
workDir = 'gs://long-gwas/nextflow-test-batch/workdir'
errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
maxRetries = 5
process.executor = 'google-batch'
process.container = 'amcalejandro/longgwas:v2'
google.location = 'us-central1'
google.project = 'gp2-data-explorer'
google.region = 'us-central1'
google.batch.spot = true
}
'gs-data' {
env {
RESOURCE_DIR = "$PWD/files"
OUTPUT_DIR = "$PWD/files/longGWAS_pipeline/results"
STORE_DIR = "$PWD/files/longGWAS_pipeline/results/cache"
ADDI_QC_PIPELINE = '/usr/src/ADDI-GWAS-QC-pipeline/addi_qc_pipeline.py'
}
process.container = 'amcalejandro/longgwas:v2'
google.region = 'us-central1'
process.executor = 'local'
}
}