nextflow.config

// Required Parameters
params.reads = "/gpfs/gibbs/pi/christakis_loan_fb343/saliva_reads/*/Unaligned/*_R{1,2}_*.fastq.gz"
//params.reads = "/vast/palmer/scratch/christakis/fb343/*/Unaligned/*_R{1,2}_*.fastq.gz"
params.ref = "/gpfs/ycga/project/christakis/fb343/databases/variant_calling_pipeline_hg38/genome.fasta"
params.outdir = "/gpfs/gibbs/pi/christakis_loan_fb343/saliva_reads/gatk"
params.snpeff_db = "hg38"
params.pl = "illumina"
params.pm = "nextseq"

process.container = 'gencorefacility/variant-calling-pipeline-gatk4'
singularity.enabled = true

// Set the Nextflow Working Directory
// By default this gets set to params.outdir + '/nextflow_work_dir'
workDir = '/vast/palmer/scratch/christakis/fb343/nextflow_work_dir'

process {
  executor = 'slurm'
  queue = 'day'
  time = '1d'
  withName:align {
    cpus = 16
    memory = 15.GB
  }
  withName:markDuplicatesSpark {
    cpus = 16
  }
}