refactor!: rename helper_gcnv_model_target_seq to helper_gcnv_targeted (

#303) (#304)
bihealth · Dec 28, 2022 · 3f36328 · 3f36328
1 parent e23e300
commit 3f36328
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Showing 6 changed files with 19 additions and 19 deletions.
diff --git a/docs/index.rst b/docs/index.rst
@@ -47,7 +47,7 @@ Project Info
     step_intro
     step_generic
     step/adapter_trimming
-    step/helper_gcnv_model_target_seq
+    step/helper_gcnv_model_targeted
     step/helper_gcnv_model_wgs
     step/hla_typing
     step/igv_session_generation

diff --git a/docs/step/helper_gcnv_model_target_seq.rst → docs/step/helper_gcnv_model_targeted.rst b/docs/step/helper_gcnv_model_target_seq.rst → docs/step/helper_gcnv_model_targeted.rst
@@ -1,7 +1,7 @@
-.. _step_helper_gcnv_model_target_seq:
+.. _step_helper_gcnv_model_targeted:
 
 =========================================
 Germline Build Target Sequence gCNV Model
 =========================================
 
-.. automodule:: snappy_pipeline.workflows.helper_gcnv_model_target_seq
+.. automodule:: snappy_pipeline.workflows.helper_gcnv_model_targeted
diff --git a/snappy_pipeline/apps/snappy_snake.py b/snappy_pipeline/apps/snappy_snake.py
@@ -22,7 +22,7 @@
     cbioportal_export,
     gene_expression_quantification,
     gene_expression_report,
-    helper_gcnv_model_target_seq,
+    helper_gcnv_model_targeted,
     helper_gcnv_model_wgs,
     hla_typing,
     igv_session_generation,
@@ -91,7 +91,7 @@
     "gene_expression_quantification": gene_expression_quantification,
     "gene_expression_report": gene_expression_report,
     "cbioportal_export": cbioportal_export,
-    "helper_gcnv_model_target_seq": helper_gcnv_model_target_seq,
+    "helper_gcnv_model_targeted": helper_gcnv_model_targeted,
     "helper_gcnv_model_wgs": helper_gcnv_model_wgs,
     "hla_typing": hla_typing,
     "igv_session_generation": igv_session_generation,

diff --git a/...ws/helper_gcnv_model_target_seq/Snakefile → ...lows/helper_gcnv_model_targeted/Snakefile b/...ws/helper_gcnv_model_target_seq/Snakefile → ...lows/helper_gcnv_model_targeted/Snakefile
@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
-"""CUBI Pipeline helper_gcnv_model_target_seq step Snakefile"""
+"""CUBI Pipeline helper_gcnv_model_targeted step Snakefile"""
 
 import os
 
 from snappy_pipeline import expand_ref
-from snappy_pipeline.workflows.helper_gcnv_model_target_seq import (
+from snappy_pipeline.workflows.helper_gcnv_model_targeted import (
     HelperBuildTargetSeqGcnvModelWorkflow,
 )
 

diff --git a/.../helper_gcnv_model_target_seq/__init__.py → ...ws/helper_gcnv_model_targeted/__init__.py b/.../helper_gcnv_model_target_seq/__init__.py → ...ws/helper_gcnv_model_targeted/__init__.py
@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
-"""Implementation of the ``helper_gcnv_model_target_seq`` step
+"""Implementation of the ``helper_gcnv_model_targeted`` step
 
-The ``helper_gcnv_model_target_seq`` step takes as the input the results of the ``ngs_mapping``
+The ``helper_gcnv_model_targeted`` step takes as the input the results of the ``ngs_mapping``
 step (aligned germline reads) and builds a model that can be used by GATK4 gCNV for a particular
 library kit.
 
@@ -79,7 +79,7 @@
 
 The default configuration is as follows.
 
-.. include:: DEFAULT_CONFIG_helper_gcnv_model_target_seq.rst
+.. include:: DEFAULT_CONFIG_helper_gcnv_model_targeted.rst
 
 """
 import os
@@ -93,12 +93,12 @@
 from snappy_pipeline.workflows.gcnv.gcnv_build_model import BuildGcnvModelStepPart
 from snappy_pipeline.workflows.ngs_mapping import NgsMappingWorkflow
 
-#: Default configuration for the helper_gcnv_model_target_seq schema
+#: Default configuration for the helper_gcnv_model_targeted schema
 DEFAULT_CONFIG = r"""
-# Default configuration helper_gcnv_model_target_seq
+# Default configuration helper_gcnv_model_targeted
 step_config:
 
-  helper_gcnv_model_target_seq:
+  helper_gcnv_model_targeted:
     path_ngs_mapping: ../ngs_mapping  # REQUIRED
 
     gcnv:
@@ -123,7 +123,7 @@ def __init__(self, parent):
 
     @dictify
     def _build_ngs_library_to_kit(self):
-        gcnv_config = DictQuery(self.w_config).get("step_config/helper_gcnv_model_target_seq/gcnv")
+        gcnv_config = DictQuery(self.w_config).get("step_config/helper_gcnv_model_targeted/gcnv")
         if not gcnv_config["path_target_interval_list_mapping"]:
             # No mapping given, we will use the "default" one for all.
             for donor in self.parent.all_donors():
@@ -175,7 +175,7 @@ class HelperBuildTargetSeqGcnvModelWorkflow(BaseStep):
     """Perform gCNV model building for WES samples by library kit"""
 
     #: Workflow name
-    name = "helper_gcnv_model_target_seq"
+    name = "helper_gcnv_model_targeted"
 
     #: Default biomed sheet class
     sheet_shortcut_class = GermlineCaseSheet
@@ -239,6 +239,6 @@ def pick_kits_and_donors(self):
     def check_config(self):
         """Check that the necessary configuration is available for the step"""
         self.ensure_w_config(
-            ("step_config", "helper_gcnv_model_target_seq", "path_ngs_mapping"),
+            ("step_config", "helper_gcnv_model_targeted", "path_ngs_mapping"),
             "Path to NGS mapping not configured but required for gCNV model building.",
         )
diff --git a/...workflows_helper_gcnv_model_target_seq.py → ...t_workflows_helper_gcnv_model_targeted.py b/...workflows_helper_gcnv_model_target_seq.py → ...t_workflows_helper_gcnv_model_targeted.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Tests for the helper_gcnv_model_target_seq workflow module code"""
+"""Tests for the helper_gcnv_model_targeted workflow module code"""
 
 import textwrap
 import unittest.mock as mock
@@ -8,7 +8,7 @@
 import ruamel.yaml as ruamel_yaml
 from snakemake.io import Wildcards
 
-from snappy_pipeline.workflows.helper_gcnv_model_target_seq import (
+from snappy_pipeline.workflows.helper_gcnv_model_targeted import (
     HelperBuildTargetSeqGcnvModelWorkflow,
 )
 
@@ -56,7 +56,7 @@ def minimal_config():
             path_target_regions: /path/to/regions.bed
             bwa:
               path_index: /path/to/bwa/index.fa
-          helper_gcnv_model_target_seq:
+          helper_gcnv_model_targeted:
             gcnv:
               path_target_interval_list_mapping:
                 - pattern: "Agilent SureSelect Human All Exon V6.*"