nextflow.config

params {
  compute_depth = true // set to `false` if you already have pre-computed and aggregated depth across all individuals. 

  // if `compute_depth = true, provide path to BAM or CRAM files. Each file must have the corresponding .bam.bai or .cram.crai index file.
  // if `compute_depth = false, provide path to files with pre-computed and aggregated depth across all individuals i.e. files generated by `aggregate` step.
  input_files = "path/to/cram/files/*.cram"
 
  // if `compute_depth = true`, list chromosomes you want to analyze

  chromosomes = ["chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr20", "chr21", "chr22"]
  
  // Thresholds for the accessibility mask
  min_dp = 10 // Minimal DP to consider for the  accessibility mask. Possible values: 1, 5, 10, 20, 30, ..., 100
  min_pct_ind = null // Minimal percent of individuals with coverage >min_dp required for the accessibility mask
  max_mean_dp = null // Maximal average depth across all individuals required for the accessibility mask
}


process {
        executor = "slurm"
        clusterOptions = "--account="
        cpus = 1
        time = "5d"
        memory = "3.5G"
}

executor {
    $slurm {
        queueSize = 1000
        jobName = { "coverage" }
}
}