config.yaml

## CSV file describing samples to process - all samples must be paired
samples: samples3.csv

## SLURM logging directory - where to write slurm output files
slurm_log_dir: slurm-logs

## Reference fasta
ref_fasta: /home/groups/carilee/refs/hg38/Homo_sapiens_assembly38.fasta

## Exome capture regions BED
capture_regions: /home/groups/carilee/refs/coverage/agilent-exonsV5/S04380110_Covered.bed

## Gene annotation database in RefFlatformat (needed for CNVkit - see tutorial website)
refFlat: /home/groups/carilee/refs/refFlat.hg38.txt.gz

## Number of threads to use for CNVKit
cnvkit_threads: 12

## Containers
# Uncomment docker paths and comment out filepaths if not in Lee Lab
# sequenza_env: docker://tbencomo/sequenza
# cnvkit_env: docker://etal/cnvkit
sequenza_env: /home/groups/carilee/software/containers/sequenza_latest.sif
cnvkit_env: /home/groups/carilee/software/containers/cnvkit_v0.9.8