anvio/anvio/workflows/ecophylo/Snakefile at master · merenlab/anvio · GitHub

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# -*- coding: utf-8
import os
import json
import os.path
import argparse

import numpy as np
import pandas as pd

import anvio
import anvio.db as db
import anvio.utils as u
import anvio.tables as t
import anvio.workflows as w

from Bio import SeqIO
from anvio.errors import ConfigError
from anvio.dbops import ContigsDatabase
from anvio.workflows.ecophylo import EcoPhyloWorkflow

__copyright__ = "Copyleft 2015-2025, The Anvi'o Project (http://anvio.org/)"
__credits__ = ["mschecht", "FlorianTrigodet"]
__license__ = "GPL 3.0"
__version__ = anvio.__version__
__maintainer__ = "Matthew S. Schechter"
__email__ = "mschechter@uchicago.edu"


M = EcoPhyloWorkflow(argparse.Namespace(config=config))
M.init()

dirs_dict = M.dirs_dict


def rule_log(rule_name, log_file_name="log"):
    """Return a canonical workflow log path under 00_LOGS/<rule_name>/."""
    if not log_file_name.endswith(".log"):
        log_file_name = f"{log_file_name}.log"

    log_path = os.path.join(dirs_dict["LOGS_DIR"], rule_name, log_file_name)

    # Ensure the per-rule log subdirectory exists. This is essential for cluster
    # submission (e.g. via clusterize), where the submit command opens the log file
    # at submission time and fails if its parent directory does not already exist.
    # Doing it here guarantees the directory exists for *every* rule that declares a
    # log, regardless of whether the rule is registered in `self.rules`.
    os.makedirs(os.path.dirname(log_path), exist_ok=True)

    return log_path


rule ECOPHYLO_WORKFLOW_target_rule:
    """The rule creates all target files for the Snakefile"""
    input:
        targets=M.target_files,


# Workflow rule modules. Keep this order to preserve existing rule dependencies.
include: w.get_workflow_rule_file_path("ecophylo", "hmm_processing.smk")
include: w.get_workflow_rule_file_path("ecophylo", "sequence_data.smk")
include: w.get_workflow_rule_file_path("ecophylo", "clustering_alignment.smk")
include: w.get_workflow_rule_file_path("ecophylo", "profile_inputs.smk")
include: w.get_workflow_rule_file_path("ecophylo", "tree_building.smk")
include: w.get_workflow_rule_file_path("ecophylo", "misc_taxonomy.smk")


if M.samples_txt_file:

    # PROFILE-MODE with read recruitment
    include: "rules/profile_mode.smk"

else:

    # TREE-MODE
    include: "rules/tree_mode.smk"