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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
icgc-argo-workflows/dnaalnqc Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// TODO nf-core: Specify your pipeline's command line flags
// Input options
input = null
local_mode = false
study_id = null
analysis_ids = null
qc_analysis_ids = null
target = false
//[gatk_contamination, samtools_stats, oxog, mosdepth, verifybamid2, collect_multiple_metrics, collect_hs_metrics, collect_wgs_metrics]
skip_tools = "mosdepth,verifybamid2"
aws_no_sign_request = false
cleanup = false
no_intervals = false
nucleotides_per_second = 200000
// Reference options
reference_base = null
fasta = null
fasta_fai = null
fasta_dict = null
germline_resource = null
germline_resource_tbi = null
bait_interval = null
target_interval = null
verifybamid2_ud = "${projectDir}/assets/verifybamid/1000g.phase3.100k.b38.vcf.gz.dat.UD"
verifybamid2_bed = "${projectDir}/assets/verifybamid/1000g.phase3.100k.b38.vcf.gz.dat.bed"
verifybamid2_mu = "${projectDir}/assets/verifybamid/1000g.phase3.100k.b38.vcf.gz.dat.mu"
autosome_non_gap = "${projectDir}/assets/autosomes_non_gap_regions.bed"
// rdpc data staging
tempdir = null
api_token = null
api_download_token = null
api_upload_token = null
song_url = null
score_url = null
song_url_download = null
score_url_download = null
song_url_upload = null
score_url_upload = null
transport_parallel = null
transport_mem = null
song_container = "ghcr.io/overture-stack/song-client"
song_container_version = "5.0.2"
score_container = "ghcr.io/overture-stack/score"
score_container_version = "5.10.0"
// Boilerplate options
outdir = null
tracedir = params.outdir ? "${params.outdir}/pipeline_info" : null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
validate_params = true
show_hidden_params = false
schema_ignore_params = 'genomes'
enable_conda = false
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '128.GB'
max_cpus = 16
max_time = '240.h'
// MultiQC options
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
}
plugins {
id "nf-amazon"
}
if (params.aws_no_sign_request) {
aws.client.anonymous = true
}
aws.client.downloadParallel = true
aws.client.maxConnections = 4
aws.batch.maxParallelTransfers = 8
if (params.cleanup) {
cleanup = true
}
profiles {
standard {
docker.enabled = true
docker.userEmulation = true
docker.registry = 'quay.io'
docker.runOptions = '-u \$(id -u):\$(id -g)'
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.engineOptions = '-s'
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
test { includeConfig 'conf/test.config' }
test_rdpc_qa { includeConfig 'conf/test_rdpc_qa.config' }
test_full { includeConfig 'conf/test_full.config' }
resource { includeConfig 'conf/resource.config' }
rdpc_qa { includeConfig 'conf/rdpc_qa.config' }
rdpc_dev { includeConfig 'conf/rdpc_dev.config' }
rdpc { includeConfig 'conf/rdpc.config' }
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// 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"
}
// Enable locally defined binary scripts for modules
nextflow.enable.moduleBinaries = true
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = params.tracedir ? true : false
file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = params.tracedir ? true : false
file = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
enabled = params.tracedir ? true : false
file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = params.tracedir ? true : false
file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'DNA Alignment QC'
author = """Linda Xiang"""
homePage = 'https://github.com/icgc-argo-workflows/dnaalnqc'
description = """ICGC-ARGO analysis workflow for post DNA alignment QC"""
mainScript = 'main.nf'
nextflowVersion = '!>=22.10.1'
version = '1.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'