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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf-core/scge Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
input = null
outdir = null
data_path = null
mgi = false
id = null
tumorid = null
normalid = null
// References
fasta = "/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/refdata/hg38_PLVM_CD19_CARv4_cd34/hg38_PLVM_CD19_CARv4_cd34.fa"
fasta_index = "${fasta}.fai"
user_group = "compute-dspencer"
queue = "dspencer"
job_group_name = "/dnidhi"
run_dragen = true
run_analysis = true
targetfile = null
// VEP annotation cache
assay_inputs {
vepcache = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/VEP_cache"
cytobands = null
hotspot_vcf = null
hotspot_vcf_index = null
}
aws_dragen_container = 'ghcr.io/dhslab/docker-dragen:el8.4.3.6'
dragen_container = "apldx/oracle8-dragen-4.3.6"
hotspot_bed = null
hotspot_csv = null
window = 200
// dragen options
alignment_file_format = 'CRAM'
mark_duplicates = true
// Dragen inputs
dragen_inputs {
dragen_hash = "/storage1/fs1/dspencer/Active/clinseq/projects/scge/data/refdata/singh_v4.3.6"
snv_noisefile = "/storage1/fs1/dspencer/Active/spencerlab/refdata/hg38/dragenfiles/IDPF_WGS_hg38_v.2.0.0_systematic_noise.snv.bed.gz"
sv_noisefile = "/storage1/fs1/dspencer/Active/spencerlab/refdata/hg38/dragenfiles/IDPF_WGS_hg38_v3.0.0_systematic_noise.sv.bedpe.gz"
dbsnp = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/dragen_align_inputs/hg38/dbsnp.vcf.gz"
dbsnp_index = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/dragen_align_inputs/hg38/dbsnp.vcf.gz.tbi"
pop_af_vcf = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/dragen_align_inputs/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz"
pop_af_vcf_index = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/dragen_align_inputs/hg38/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi"
dragen_adapter1 = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/dragen_align_inputs/hg38/dragen_adapter1.fa"
dragen_adapter2 = "/storage1/fs1/dspencer/Active/clinseq/projects/chromoseq/refdata/dragen_align_inputs/hg38/dragen_adapter2.fa"
input_cram_reference = "${params.fasta}"
input_cram_reference_index = "${params.fasta_index}"
}
// TODO nf-core: Specify your pipeline's command line flags
// Input options
// References
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf-core/scge custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/scge.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/scge profiles: ${params.custom_config_base}/pipeline/scge.config")
// }
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
id 'nf-amazon'
}
aws {
region = 'us-east-1'
batch {
cliPath = '/home/centos/miniconda/bin/aws'
volumes = ['/staging','/dev/shm:/dev/shm']
}
accessKey = secrets.AWS_ACCESS_KEY
secretKey = secrets.AWS_SECRET_KEY
}
profiles {
stub { includeConfig 'conf/stub.config' } // local executor for testing
ris {
executor.queueSize = 20
executor.submitRateLimit = '1/1sec'
process {
executor = "lsf"
clusterOptions = { "-a 'docker(${task.container})' -q ${params.queue} -G ${params.user_group} -g ${params.job_group_name}" }
}
}
dragen2 {
process {
withLabel: 'dragen' {
queue = { "dragen-2" }
memory = 200.GB
cpus = 20
time = 16.h
clusterOptions = { "-a 'gtac-mgi-dragen(${params.dragen_container})' -m compute1-dragen-2 -G ${params.user_group} -g ${params.job_group_name} -env 'all, LSF_DOCKER_DRAGEN=y'" }
ext.intermediate_dir = '/staging/intermediate-results-dir'
}
}
}
dragen4 {
process {
withLabel: 'dragen' {
queue = { "dragen-4" }
memory = 400.GB
cpus = 30
time = 16.h
clusterOptions = { "-a 'gtac-mgi-dragen(${params.dragen_container})' -m compute1-dragen-4 -G ${params.user_group} -g ${params.job_group_name} -env 'all, LSF_DOCKER_DRAGEN=y'" }
ext.intermediate_dir = '/staging/intermediate-results-dir'
}
}
}
dragenaws {
process {
withLabel: dragenalign {
executor = 'awsbatch'
ext.dragen_aws_image = "${params.aws_dragen_container}"
ext.dragen_license_args = "--lic-server 'https://${secrets.AWS_DRAGEN_USER}:${secrets.AWS_DRAGEN_PASSWORD}@license.edicogenome.com'"
queue = 'nextflow-dragen-oracle8'
containerOptions = '--privileged --ulimit nofile=65535:65535 --ulimit nproc=16384:16384'
maxErrors = 1
cpus = 16
memory = 230.GB
time = 24.h
ext.intermediate_dir = '/staging/intermediate-results-dir'
}
}
}
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
channels = ['conda-forge', 'bioconda', 'defaults']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'quay.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id 'nf-amazon'
}
aws {
region = 'us-east-1'
batch {
cliPath = '/home/ec2-user/miniconda/bin/aws'
volumes = ['/staging','/dev/shm:/dev/shm']
}
accessKey = secrets.AWS_ACCESS_KEY
secretKey = secrets.AWS_SECRET_KEY
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {
params.genomes = [:]
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf-core/scge'
author = """Nidhi"""
homePage = 'https://github.com/nf-core/scge'
description = """Nextflow implementation of scge workflow"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}