From 4d7dbd25ba690aba8291c5da85aba92730409c51 Mon Sep 17 00:00:00 2001 From: Till Hartmann Date: Wed, 27 Mar 2024 16:47:49 +0100 Subject: [PATCH] isort, black --- snappy_pipeline/base.py | 11 ++++++----- .../workflows/adapter_trimming/__init__.py | 2 +- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/snappy_pipeline/base.py b/snappy_pipeline/base.py index 5bfa2f010..03b455824 100644 --- a/snappy_pipeline/base.py +++ b/snappy_pipeline/base.py @@ -2,13 +2,13 @@ """Basic utility code for snappy_pipeline """ -import os -import sys -import warnings from collections import OrderedDict from collections.abc import MutableMapping from copy import deepcopy +import os +import sys from typing import Any +import warnings import ruamel.yaml as ruamel_yaml from snakemake.utils import validate @@ -72,8 +72,9 @@ def expand_ref(config_path, dict_data, lookup_paths=None, dict_class=OrderedDict def validate_config(config: dict[Any, Any], workflow: str, file=sys.stderr): print(f"\nValidating config.yaml for {workflow}", file=file) - config_schema_path = os.path.join(os.path.dirname(snakefile_path(workflow)), - "config.schema.yaml") + config_schema_path = os.path.join( + os.path.dirname(snakefile_path(workflow)), "config.schema.yaml" + ) validate(config, config_schema_path) diff --git a/snappy_pipeline/workflows/adapter_trimming/__init__.py b/snappy_pipeline/workflows/adapter_trimming/__init__.py index 6ca32396d..8e54b4843 100644 --- a/snappy_pipeline/workflows/adapter_trimming/__init__.py +++ b/snappy_pipeline/workflows/adapter_trimming/__init__.py @@ -142,8 +142,8 @@ from biomedsheets.shortcuts import GenericSampleSheet from snakemake.io import expand -from snappy_pipeline.utils import dictify, listify from snappy_pipeline.base import validate_config +from snappy_pipeline.utils import dictify, listify from snappy_pipeline.workflows.abstract import ( BaseStep, BaseStepPart,