barrydigby/dnaseq_references

DNAseq References for GRCh37, 38

Create reference data for Somatic_n-of-1 NextFlow pipeline

How to Setup

Dependencies:

NextFlow, Singularity

Reference Generation:

nextflow run BarryDigby/DNAseq_references

Optional arguments:
  --version   STRING    GRCh37 or GRCh38 (default)
  --outDir    STRING    output directory path; NB ${params.version} dir is created therein
  --exometag    STRING    naming for exome outputs when supplied; tag is then used in somatic_n-of-1 and batch_somatic pipelines to select relevant exome data
  and either
  --exomebedurl     STRING      URL to exome bed file for intervals; NB assumes GRCh37
  or
  --exomebedfile     STRING      locally downloaded exome bed file for intervals; NB assumes GRCh37