config.yaml

# This file allows you to configure the workflow to suit your needs.

# Some things you can customize are:
# - Fill in the name of your reference genome [required]
# - Parameters for splitting the reference genome into regions to process in parallel
# - Filename for those regions to be stored
# - How many threads to use for fastq-dumping, trimming, aligning, and variant calling
# - How much memory samtools sort is allowed to use

# Tab-delimited file of unit and sample info [required]
# See README for how to create this file.
units: "units.tsv"
# Please fill in the path to your reference genome assembly [required].
genome: "data/genome/yourgenome.fa"

# In order to speed up variant calling, the reference genome will be
# split into small chunks that can be processed in parallel.
# To avoid splitting in the middle of a contig, we want to split where there are
# gaps in the assembly -- for example, 4000 or more N's in a row.
intervals:
  # Minimum number of N's in a row to split into separate regions
  gap_length: 4000
  # Filename for the workflow should store list of regions
  file: "data/intervals/intervals.bed"

# If you have raw .sra files from NCBI Sequence Read Archive (e.g., from prefetch),
# the workflow can convert them to fastq for you.
# If you already have fastq files, put them in data/reads/ and this step will be skipped.
fastq_dump:
    threads: 8
    # Folder where you downloaded .sra files
    sra_location: "data/sra/"

# Parameters for cutadapt and cutadapt_pe rules.
cutadapt:
    threads: 8
    # 3' adapter sequence to remove from all reads.
    # See cutadapt documentation for -a and -A options.
    adapter: "AGATCGGAAGAGC"
    # Base quality trimming cutoff. See cutadapt documentation for -q option.
    qual: 10

# Parameters for align rule.
align:
    # Cores that BWA will use for each instance of rule align
    threads: 12
    # Maximum memory per thread for samtools sort; suffix K/M/G recognized
    sort_mem: 2G

# Parameters for call_variants rule.
freebayes:
    # Freebayes command-line options
    options: "--hwe-priors-off --min-mapping-quality 41 --min-base-quality 20 --genotype-qualities"