gene_expression_report: fix tests

bihealth · May 29, 2024 · 91745c3 · 91745c3
1 parent ae49bdf
commit 91745c3
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/tests/snappy_pipeline/workflows/test_workflows_gene_expression_report.py b/tests/snappy_pipeline/workflows/test_workflows_gene_expression_report.py
@@ -30,7 +30,10 @@ def minimal_config():
               path_index: /path/to/star/index
 
           gene_expression_quantification:
+            path_ngs_mapping: ../ngs_mapping
             tools: ['strandedness']
+            strandedness:
+              path_exon_bed: /path/to/exon.bed
 
           gene_expression_report:
             path_gene_expression_quantification: /work
@@ -56,11 +59,13 @@ def gene_expression_report_workflow(
     work_dir,
     config_paths,
     cancer_sheet_fake_fs,
+    aligner_indices_fake_fs,
     mocker,
 ):
     """Return GeneExpressionReportWorkflow object pre-configured with cancer sheet"""
     # Patch out file-system related things in abstract (the crawling link in step is defined there)
     patch_module_fs("snappy_pipeline.workflows.abstract", cancer_sheet_fake_fs, mocker)
+    patch_module_fs("snappy_pipeline.workflows.ngs_mapping", aligner_indices_fake_fs, mocker)
     dummy_workflow.globals = {
         "ngs_mapping": lambda x: "NGS_MAPPING/" + x,
         "gene_expression_quantification": lambda x: "GENE_EXPRESSION_QUANTIFICATION/" + x,