config.yaml

# Input data
# ----------
# These parameters control what trait data and what
# variants will be used for the GWAS.
traits: traits.tsv
variants: test/data/variants.vcf.gz

# Symlinking of data
# ------------------
# If the location of the variant data is not
# writeable for the user, then it can be
# necessary to symlink the data to a different
# location. This also has other advantages, and
# is therefore done by default.
symlink_data: true
symlink_dir: data

# PLINK prefix
# ------------
# A prefix for PLINK output files can be specified.
# If not given, this will be based on the name of
# the VCF file. Note that if a PLINK prefix is
# specified, and that set of files already exist,
# none of the SNP filtering parameters below will
# be applied, but the variants will be used as-is.
#
# plink_prefix: test/data/variants

# SNP filtering
# -------------
# These parameters are used for filtering the variants
# that go into the GWAS.
snp_filtering:
    # Minor allele frequency threshold
    maf: 0.05
    # Hardy-Weinberg equilibrium p-value threshold
    hwe_p: 0.000001

# PLINK parameters
# ----------------
#
plink:
    # Allow for non-standard chromosome names
    allow_extra_chr: false
    # How to generate family IDs from VCF sample IDs
    family_id_flags: --double-id

# Cluster configuration
# ---------------------
# Cookiecutter profile generation for cluster
# environments. Required parameters:
#
# - cookiecutter_url: url to the cookiecutter template
#   of a profile (see https://github.com/Snakemake-Profiles
#   for some available profiles).
# - profile_name: desired name of the generated profile.
# - use-conda: whether conda should be used for managing
#   software dependencies.
# - restart-times: how many times snakemake should try to
#   restart failing jobs.
# - jobs: maximum number of concurrent jobs to submit to
#   the cluster.
# - latency-wait: maximum time (in seconds) that snakemake
#   waits for missing output files.
#
# Other parameter are specific to the cookiecutter.json
# file in the cookiecutter template.
cluster:
    cookiecutter_url: https://github.com/Snakemake-Profiles/slurm
    profile_name: test_slurm
    use-conda: true
    restart-times: 0
    jobs: 100
    latency-wait: 120

    # Parameters specific for the cookiecutter template
    account: testaccount
    output: "logs/slurm-%j.out"
    error: "logs/slurm-%j.err"
    partition: core
    submit_script: slurm-submit-advanced.py