nextflow.config

// Required Parameters
// Path to your input file in the format (including header names) shown in the example input file
params.input_file = "/path/to/repo/example_input.csv"

params.ref = "/scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa"
params.outdir = "/scratch/$USER/gatk_hc_pipeline/a"
params.snpeff_db = "Saccharomyces_cerevisiae"
params.pl = "illumina"
params.pm = "nextseq"

// Which results to export into the outdir
params.export_aligned_reads = false
params.export_dedup_sorted = false
params.export_metrics = true
params.export_snps = true
params.export_indels = true
params.export_bqsr = false
params.export_covariates = false
params.export_snpeff = false

// Set the Nextflow Working Directory
// By default this gets set to params.outdir + '/nextflow_work_dir'
workDir = params.outdir + '/nextflow_work_dir'

singularity.autoMounts = true