Snakefile

"""
This is the main phylogenetic Snakefile that orchestrates the full phylogenetic
workflow and defines its default output(s).
"""
# The workflow filepaths are written relative to this Snakefile's base directory
workdir: workflow.current_basedir

# Use default configuration values. Override with Snakemake's --configfile/--config options.
configfile: "defaults/config.yaml"


# This is the default rule that Snakemake will run when there are no specified targets.
# The default output of the phylogenetic workflow is usually the final
# Nexstrain dataset(s) or Auspice JSON(s) that are output from `rules/export.smk`
# See Nextstrain docs on expected naming conventions of dataset files
# https://docs.nextstrain.org/page/reference/data-formats.html
rule all:
    input:
        # Fill in path(s) to the final exported Auspice JSON(s)
        auspice_json="auspice/rabies.json",


# These rules are imported in the order that they are expected to run.
# Each Snakefile will have documented inputs and outputs that should be kept as
# consistent interfaces across pathogen repos. This allows us to define typical
# steps that are required for a phylogenetic workflow, but still allow pathogen
# specific customizations within each step.
# Note that only PATHOGEN level customizations should be added to these
# core steps, meaning they are custom rules necessary for all builds of the pathogen.
# If there are build specific customizations, they should be added with the
# custom_rules imported below to ensure that the core workflow is not complicated
# by build specific rules.
include: "rules/prepare_sequences.smk"
include: "rules/construct_phylogeny.smk"
include: "rules/annotate_phylogeny.smk"
include: "rules/export.smk"

# Allow users to import custom rules provided via the config.
# This allows users to run custom rules that can extend or override the workflow.
# A concrete example of using custom rules is the extension of the workflow with
# rules to support the Nextstrain automation that upload files and send internal
# Slack notifications.
# For extensions, the user will have to specify the custom rule targets when
# running the workflow.
# For overrides, the custom Snakefile will have to use the `ruleorder` directive
# to allow Snakemake to handle ambiguous rules
# https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#handling-ambiguous-rules
if "custom_rules" in config:
    for rule_file in config["custom_rules"]:

        include: rule_file