copier.yml

_min_copier_version: "6.0.0"
_answers_file: ".copier-answers.yml"

# CONFIGURATION -------------------------
_exclude:
  - "*"
  - "!config"
  - "!config/**"
  - "!images"
  - "!images/*.pdf"
  - "!workflow"
  - "!workflow/**"
  - "!.dockerignore"
  - "!.editorconfig"
  - "!Dockerfile"
  - "!README.md"
  - "!.copier-answers.yml"
  - "!docker-compose.yml"
  
_jinja_extensions:
  - "jinja2_time.TimeExtension"

# _tasks:
#   - "mkdir resources"
  
# QUESTIONS FOR USER -------------------------
species:
  type: str
  help: Give the species whose reference genome we are obtaining
  default: caenorhabditis_elegans
  choices:
    "Human (H. sapiens)": "homo_sapiens"
    "Mouse (M. musculus)": "mus_musculus"
    "Zebrafish (D. rerio)": "danio_rerio"
    "Worm (C. elegans)": "caenorhabditis_elegans"
    "Fruitfly (D. melanogaster)": "drosophila_melanogaster"
    "Mouse Lemur (M. murinus)": "microcebus_murinus"
    # "Mouse 129S1/SvImJ": "mus_musculus_129s1svimj"
    # "Mouse A/J": "mus_musculus_aj"
    # "Mouse AKR/J": "mus_musculus_akrj"
    # "Mouse BALB/cJ": "mus_musculus_balbcj"
    # "Mouse C3H/HeJ": "mus_musculus_c3hhej"
    # "Mouse C57BL/6NJ": "mus_musculus_c57bl6nj"
    # "Mouse CAST/EiJ": "mus_musculus_casteij"
    # "Mouse CBA/J": "mus_musculus_cbaj"
    # "Mouse DBA/2J": "mus_musculus_dba2j"
    # "Mouse FVB/NJ": "mus_musculus_fvbnj"
    # "Mouse LP/J": "mus_musculus_lpj"
    # "Mouse NOD/ShiLtJ": "mus_musculus_nodshiltj"
    # "Mouse NZO/HlLtJ": "mus_musculus_nzohlltj"
    # "Mouse PWK/PhJ": "mus_musculus_pwkphj"
    # "Mouse WSB/EiJ": "mus_musculus_wsbeij"

date:
  type: str
  help: Specify the date to use for naming project directories
  default: "{% now 'utc', '%Y-%m-%d' %}"
  placeholder: "{% now 'utc', '%Y-%m-%d' %}"