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nextflow.config
executable file
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nextflow.config
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params {
reference_vcfs = "/path/to/phased/reference/genotypes/hgdp1kgp_chr*.{bcf,vcf}*" // VCF/BCF files with phased reference genotypes and their tbi/csi indices. The phased reference genotypes must be split by chromosome and prefixed with: chr1., chr2., ..., chr22., chrX_nonpar., chrX_par1., chrX_par2.
reference_sites_vcfs = "/lustre06/project/6061810/shared/HGDP_1KG_phased/hgdp1kgp_chr*.sites.vcf.gz*" // VCF files with reference sites (no genotypes) and tbi indices. Must be split by chromosome in a similar way as the phased genotypes.
study_bams = "/path/to/study/bam_or_cram_files/*.{bam,cram}*" // BAM/CRAM files for study samples (one per sample) and the corresponing bai/crai indices.
// If you don't plan to impute chromosome X, then you can ignore this argument
study_sample_ploidy = "/path/to/study/chrX_ploidy.txt" // Text file listing sample ploidy in chromosome X. No header; space-delimited; one sample per line; two columns - sample name and number of chrX copies (1 or 2). You can estimate the ploidy of chromosome X from chromosome X sequencing depth.
referenceDir = "/path/to/referenceGenome/folder"
referenceGenome = "<filename>.fa"
gatkContainer = "/path/to/gatk.sif"
window_size = 2000000
buffer_size = 200000
chunk_exec = "/path/to/GLIMPSE/bin/GLIMPSE_chunk"
phase_exec = "/path/to/GLIMPSE/bin/GLIMPSE_phase"
ligate_exec = "/path/to/GLIMPSE/bin/GLIMPSE_ligate"
glimpse_maps = "/path/to/GLIMPSE/maps/genetic_maps.b38/"
}
apptainer {
enabled = true
autoMounts = true
}
process {
executor = "slurm"
// cluster allocation account name
//clusterOptions = "--account="
//executor = "local"
cpus = 1
time = "12h"
memory = "4GB"
}
executor {
$slurm {
queueSize = 1000
jobName = { "imputation" }
}
$local {
cpus = 1
}
}