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bihealth · Jun 22, 2021 · c959e52 · c959e52
1 parent 16ddfe2
commit c959e52
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Showing 20 changed files with 39 additions and 39 deletions.
diff --git a/snappy_pipeline/workflows/abstract/__init__.py b/snappy_pipeline/workflows/abstract/__init__.py
@@ -276,7 +276,7 @@ def _cached_read_generic_tsv_sheet(path_abs, path_rel, naming_scheme):
 @lru_cache()
 def _cached_yaml_round_trip_load_str(str_value):
     """Cached reading of YAML ``str`` objects."""
-    #return yaml.round_trip_load(StringIO(str_value))
+    # return yaml.round_trip_load(StringIO(str_value))
     yaml_ = yaml.YAML()
     return yaml_.load(str_value)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_abstract.py b/tests/snappy_pipeline/workflows/test_workflows_abstract.py
@@ -128,7 +128,7 @@ def test_link_in_path_generator(germline_sheet_fake_fs, config_lookup_paths, wor
 def dummy_config():
     """Return dummy configuration OrderedDicts"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         step_config: {}
         static_data_config: {}
         data_sets:
@@ -141,7 +141,7 @@ def dummy_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_gene_expression_quantification.py b/tests/snappy_pipeline/workflows/test_workflows_gene_expression_quantification.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -41,7 +41,7 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_hla_typing.py b/tests/snappy_pipeline/workflows/test_workflows_hla_typing.py
@@ -18,7 +18,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -32,7 +32,7 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py b/tests/snappy_pipeline/workflows/test_workflows_ngs_mapping.py
@@ -23,7 +23,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -51,7 +51,7 @@ def minimal_config():
             naming_scheme: only_secondary_id
             pedigree_field: pedigree_field
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_roh_calling.py b/tests/snappy_pipeline/workflows/test_workflows_roh_calling.py
@@ -19,7 +19,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -50,7 +50,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_msi_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_msi_calling.py
@@ -18,7 +18,7 @@
 def minimal_config():
     """Return YAML parsing result for configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -43,7 +43,7 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_targeted_seq_cnv_calling.py
@@ -23,7 +23,7 @@
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -54,7 +54,7 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_calling.py
@@ -19,7 +19,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -53,7 +53,7 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_wgs_cnv_calling.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -59,7 +59,7 @@ def minimal_config():
             type: matched_cancer
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_targeted_seq_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_targeted_seq_cnv_calling.py
@@ -79,7 +79,7 @@ def get_expected_gcnv_log_file(step_name):
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -120,7 +120,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_annotation.py b/tests/snappy_pipeline/workflows/test_workflows_variant_annotation.py
@@ -18,7 +18,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -47,7 +47,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_calling.py b/tests/snappy_pipeline/workflows/test_workflows_variant_calling.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -54,7 +54,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/...py_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py b/...py_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_annotation.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -51,7 +51,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py b/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_calling.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -51,7 +51,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py b/...nappy_pipeline/workflows/test_workflows_variant_denovo_filtration_from_variant_phasing.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -51,7 +51,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_phasing.py b/tests/snappy_pipeline/workflows/test_workflows_variant_phasing.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -58,7 +58,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_cnv_calling.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (germline) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -53,7 +53,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_wgs_mei_calling.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_mei_calling.py
@@ -20,7 +20,7 @@
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -52,7 +52,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)
 

diff --git a/tests/snappy_pipeline/workflows/test_workflows_wgs_sv_calling.py b/tests/snappy_pipeline/workflows/test_workflows_wgs_sv_calling.py
@@ -19,7 +19,7 @@
 def minimal_config():
     """Return YAML parsing result for (somatic) configuration"""
     config_str = textwrap.dedent(
-            r"""
+        r"""
         static_data_config:
           reference:
             path: /path/to/ref.fa
@@ -52,7 +52,7 @@ def minimal_config():
             type: germline_variants
             naming_scheme: only_secondary_id
         """
-        ).lstrip()
+    ).lstrip()
     yaml_ = yaml.YAML()
     return yaml_.load(config_str)