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liftover.config
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/*
* -------------------------------------------------
* Nextflow config file for running tests
* -------------------------------------------------
* Defines bundled input files and everything required
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/methylseq -profile test
*/
params {
project_name = 'refimpute'
project_description = 'A simple imputation run on chrm 6 distributed with git repo'
homedir = "${HOME}/imputation" // homedir: Path to your script, where the nextflow main script is located
outdir = "/cbio/projects/001/clients/${project_name}/data" // outDir: where to put all pipeline's outputs
workdir = "/scratch3/users/mamana/${project_name}/work" // wordDir: Nextflow working directory
scratch = "/scratch3/users/mamana/${project_name}/"
help = false
max_memory = 2.GB
max_cpus = 2
max_time = 48.h
// Reference panels
ref_panels = [
["H3AR6x", "/cbio/dbs/refpanels/H3AR6x/m3vcfs/H3AR6x_%s_phased.m3vcf.gz", "/cbio/dbs/refpanels/H3AR6x/bcfs/H3AR6x_%s_phased.bcf","/cbio/dbs/refpanels/H3AR4a/metadata/all.v4.meta.updated"],
]
// datasets extracted already, all chromosomes in one [name, vcf_file]
vcf_files = [
// ['awigen_ref_qc_b38', "/cbio/projects/001/clients/refimpute/data/awigen_qc_sort.hg38_final.vcf.gz"],
['awigen_500', "/cbio/projects/001/clients/refimpute/data/awigen_500.vcf.gz"],
['awigen_1000', "/cbio/projects/001/clients/refimpute/data/awigen_1000.vcf.gz"],
['awigen_2000', "/cbio/projects/001/clients/refimpute/data/awigen_2000.vcf.gz"],
['awigen_4000', "/cbio/projects/001/clients/refimpute/data/awigen_4000.vcf.gz"],
['awigen_7000', "/cbio/projects/001/clients/refimpute/data/awigen_7000.vcf.gz"],
['awigen_100wgs', "/cbio/projects/001/clients/refimpute/data/awigen_wgs/awigen_recal-SNP_recal-INDEL_filter-pass.vcf.gz"],
['ggvp_wgs', "/cbio/projects/001/clients/refimpute/data/GGVP/ggvp_downsized_final.vcf.gz"],
['ssmp_wgs', '/cbio/projects/001/clients/refimpute/data/SSMP/SSMP-autosomal.vcf.gz']
]
map_files = [
["H3AFRICAv1_qc_awigen", "/cbio/projects/001/clients/refimpute/data/awigen-qc.bim.pos"],
["axiom", "/cbio/projects/001/clients/refimpute/data/chips/axiom.pos"],
["mega", "/cbio/projects/001/clients/refimpute/data/chips/mega.pos"],
["omni", "/cbio/projects/001/clients/refimpute/data/chips/omni.pos"],
]
// Genome build
genome_build = "b37"
// Genetic map for eagle2
// eagle_genetic_map = "/cbio/dbs/eagle2/genetic_map_hg38_withX.txt.gz"
// eagle_genetic_map = "/cbio/dbs/refpanels/eagle/tables/genetic_map_hg19_withX.txt.gz"
chain_file = "/cbio/users/mamana/reference/liftover/GRCh37/GRCh37_to_GRCh38.chain.gz"
// Reference genome used for QC
reference_genome = "/cbio/dbs/gatk/hg38/Homo_sapiens_assembly38.fasta"
// reference_genome = "/cbio/users/mamana/reference/gatk_bundle/human_g1k_v37_decoy.fasta"
//// chromosome mapping for liftover one by ine 1 chr1\n 2 chr2
chromosome_mapping = "/cbio/users/mamana/reference/chromosome_mapping_b37_b38.txt"
// Use ALL or '' to use all available chromosome in the target dataset
// chromosomes = "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22"
// chromosomes = "chr22"
// imputation parameters
chunk_size = "25000000" // in base
buffer_size = "500000" // in base
// QC parameters
site_miss = "0.05"
hwe = "0.00001"
mac = "1"
info_cutoff = '0.6'
min_ac = '2'
min_alleles = '2'
max_alleles = '2'
// Phasing method: shapeit (default) or eagle2
phasing_method = "eagle"
// Imputation method minimac4 (default) or IMPUTE2
impute_method = "minimac4"
// Minimac4 option
minRatio = '0.001'
// Phasing method: eagle2 (default) or shapeit
phasing_method = "eagle"
// Plink to use, sometimes it can be plink2
plink="plink2"
}
timeline {
enabled = true
file = "${params.outdir}/nextflow_reports/${params.project_name}_h3achipimputation_timeline.html"
}
report {
enabled = true
file = "${params.outdir}/nextflow_reports/${params.project_name}_h3achipimputation_report.html"
}
trace {
enabled = true
file = "${params.outdir}/nextflow_reports/${params.project_name}_h3achipimputation_trace.txt"
}
// dag {
// enabled = true
// file = "${params.outdir}/nextflow_reports/${params.project_name}_h3achipimputation_dag.pdf"
// }
process {
// Process-specific resource requirements
withLabel: 'crossmap' {
errorStrategy = { if (task.exitStatus in [143, 137, 255]) { 'retry' } else { 'terminate' } }
memory = 5.GB
cpus = 1
container = 'docker://quay.io/mypandos/crossmap:latest'
}
withLabel : 'bcftools' {
errorStrategy = { if (task.exitStatus in [143, 137, 255]) { 'retry' } else { 'terminate' } }
cpus = 2
memory = 50.GB
container = 'docker://quay.io/mypandos/bcftools'
}
withLabel : 'large' {
errorStrategy = { if (task.exitStatus in [143, 137, 255]) { 'retry' } else { 'terminate' } }
cpus = { 2 * task.attempt }
memory = 50.GB
}
withLabel : 'verylarge' {
errorStrategy = { if (task.exitStatus in [143, 137, 255]) { 'retry' } else { 'terminate' } }
cpus = { 3 * task.attempt }
memory = 50.GB
maxForks = 70
}
}
profiles{
singularity {
singularity.enabled = true
singularity.autoMounts = true
singularity.cacheDir = "/cbio/users/mamana/singularity-containers"
process.container = 'docker://quay.io/mypandos/crossmap:latest'
singularity.runOptions = " -B ${params.scratch} -B /cbio/users/mamana " // add any paths that need to be mounted here
}
slurm {
executor{
queueSize = 100
}
process{
executor = 'slurm'
queue = 'Main'
memory = { 30.GB * task.attempt }
cpus = 2
time = { 72.h * task.attempt }
maxForks = 70
stageOutMode = 'rsync'
maxRetries = 0
errorStrategy = 'retry'
clusterOptions = { "--mail-user=mbymam001@myuct.ac.za" }
}
}
}