Replied isort

bihealth · Apr 7, 2021 · 258d1df · 258d1df
1 parent 2282680
commit 258d1df
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Showing 3 changed files with 16 additions and 7 deletions.
diff --git a/snappy_pipeline/workflows/abstract/__init__.py b/snappy_pipeline/workflows/abstract/__init__.py
@@ -25,8 +25,8 @@
 from snakemake.io import touch
 
 from snappy_pipeline.base import (
-    merge_dicts,
     MissingConfiguration,
+    merge_dicts,
     print_config,
     print_sample_sheets,
     snakefile_path,

diff --git a/snappy_pipeline/workflows/ngs_mapping/__init__.py b/snappy_pipeline/workflows/ngs_mapping/__init__.py
@@ -281,6 +281,7 @@
 from snakemake.io import expand
 
 from snappy_pipeline.base import InvalidConfiguration
+from snappy_pipeline.utils import DictQuery, dictify, listify
 from snappy_pipeline.workflows.abstract import (
     STDERR_TO_LOG_FILE,
     BaseStep,
@@ -290,8 +291,6 @@
     LinkOutStepPart,
     get_ngs_library_folder_name,
 )
-from snappy_pipeline.utils import DictQuery, dictify, listify
-
 
 __author__ = "Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>"
 
@@ -1086,7 +1085,9 @@ def get_result_files(self):
             ),
         )
         yield from self._yield_result_files(
-            os.path.join("output", name_pattern, "report", "bam_qc", name_pattern + ".bam.{report}.txt"),
+            os.path.join(
+                "output", name_pattern, "report", "bam_qc", name_pattern + ".bam.{report}.txt"
+            ),
             report=("bamstats", "flagstats", "idxstats"),
         )
         yield from self._yield_result_files(
@@ -1096,7 +1097,9 @@ def get_result_files(self):
             report=("bamstats", "flagstats", "idxstats"),
         )
         yield from self._yield_result_files(
-            os.path.join("output", name_pattern, "report", "bam_qc", name_pattern + ".bam.bamstats.html")
+            os.path.join(
+                "output", name_pattern, "report", "bam_qc", name_pattern + ".bam.bamstats.html"
+            )
         )
         yield from self._yield_result_files(
             os.path.join(
@@ -1115,6 +1118,9 @@ def get_result_files(self):
                     )
                     # Per-sample target coverage report.
                     yield from expand(
+                        os.path.join(
+                            "output", name_pattern, "report", "cov_qc", name_pattern + ".{ext}"
+                        ),
                         mapper=self.config["tools"][extraction_type.lower() + suffix],
                         ngs_library=[ngs_library],
                         ext=["txt", "txt.md5"],
@@ -1126,7 +1132,9 @@ def get_result_files(self):
             and self.config["picard_hs_metrics"]["path_baits_interval_list"]
         ):
             yield from self._yield_result_files(
-                os.path.join("output", name_pattern, "report", "picard_hs_metrics", name_pattern + ".txt")
+                os.path.join(
+                    "output", name_pattern, "report", "picard_hs_metrics", name_pattern + ".txt"
+                )
             )
             yield from self._yield_result_files(
                 os.path.join(

diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py
@@ -6,12 +6,13 @@
 import io
 import textwrap
 
-from biomedsheets.io_tsv import read_germline_tsv_sheet, read_generic_tsv_sheet
+from biomedsheets.io_tsv import read_generic_tsv_sheet, read_germline_tsv_sheet
 import pytest
 import ruamel.yaml as yaml
 from snakemake.io import Wildcards
 
 from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow
+
 from .common import get_expected_log_files_dict
 from .conftest import patch_module_fs