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# coding: utf-8
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- import os
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import re
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from pathlib import Path
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- import snakemake as sm
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- from snakemake .script import Snakemake
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-
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class Dict (dict ):
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"""
@@ -92,6 +88,19 @@ def mock_snakemake(
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keyword arguments fixing the wildcards. Only necessary if wildcards are
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needed.
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"""
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+ import os
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+
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+ import snakemake as sm
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+ from snakemake .api import Workflow
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+ from snakemake .common import SNAKEFILE_CHOICES
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+ from snakemake .script import Snakemake
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+ from snakemake .settings .types import (
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+ ConfigSettings ,
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+ DAGSettings ,
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+ ResourceSettings ,
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+ StorageSettings ,
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+ WorkflowSettings ,
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+ )
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script_dir = Path (__file__ ).parent .resolve ()
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if root_dir is None :
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f" { root_dir } or scripts directory { script_dir } "
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)
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try :
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- for p in sm . SNAKEFILE_CHOICES :
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+ for p in SNAKEFILE_CHOICES :
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if os .path .exists (p ):
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snakefile = p
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break
@@ -120,12 +129,12 @@ def mock_snakemake(
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elif isinstance (configfiles , str ):
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configfiles = [configfiles ]
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- resource_settings = sm . ResourceSettings ()
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- config_settings = sm . ConfigSettings (configfiles = map (Path , configfiles ))
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- workflow_settings = sm . WorkflowSettings ()
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- storage_settings = sm . StorageSettings ()
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- dag_settings = sm . DAGSettings (rerun_triggers = [])
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- workflow = sm . Workflow (
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+ resource_settings = ResourceSettings ()
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+ config_settings = ConfigSettings (configfiles = map (Path , configfiles ))
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+ workflow_settings = WorkflowSettings ()
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+ storage_settings = StorageSettings ()
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+ dag_settings = DAGSettings (rerun_triggers = [])
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+ workflow = Workflow (
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config_settings ,
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resource_settings ,
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workflow_settings ,
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