diff --git a/docs/index.rst b/docs/index.rst index 1dbaf4844..180ac1279 100644 --- 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 b/docs/step/helper_gcnv_model_targeted.rst similarity index 80% rename from docs/step/helper_gcnv_model_target_seq.rst rename to docs/step/helper_gcnv_model_targeted.rst index 3d3d1be83..4a86f7c0d 100644 --- a/docs/step/helper_gcnv_model_target_seq.rst +++ b/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 index 2cb851aae..45e1cbce2 100644 --- 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/snappy_pipeline/workflows/helper_gcnv_model_target_seq/Snakefile b/snappy_pipeline/workflows/helper_gcnv_model_targeted/Snakefile similarity index 97% rename from snappy_pipeline/workflows/helper_gcnv_model_target_seq/Snakefile rename to snappy_pipeline/workflows/helper_gcnv_model_targeted/Snakefile index 3205673b3..0903c7753 100644 --- a/snappy_pipeline/workflows/helper_gcnv_model_target_seq/Snakefile +++ b/snappy_pipeline/workflows/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/snappy_pipeline/workflows/helper_gcnv_model_target_seq/__init__.py b/snappy_pipeline/workflows/helper_gcnv_model_targeted/__init__.py similarity index 94% rename from snappy_pipeline/workflows/helper_gcnv_model_target_seq/__init__.py rename to snappy_pipeline/workflows/helper_gcnv_model_targeted/__init__.py index 2794bd37c..24ad54551 100644 --- a/snappy_pipeline/workflows/helper_gcnv_model_target_seq/__init__.py +++ b/snappy_pipeline/workflows/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/tests/snappy_pipeline/workflows/test_workflows_helper_gcnv_model_target_seq.py b/tests/snappy_pipeline/workflows/test_workflows_helper_gcnv_model_targeted.py similarity index 99% rename from tests/snappy_pipeline/workflows/test_workflows_helper_gcnv_model_target_seq.py rename to tests/snappy_pipeline/workflows/test_workflows_helper_gcnv_model_targeted.py index 511bfbf4c..4b44518f0 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_helper_gcnv_model_target_seq.py +++ b/tests/snappy_pipeline/workflows/test_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.*"