fix more test paths

bihealth · Dec 6, 2024 · b9834cb · b9834cb
1 parent 5725566
commit b9834cb
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py
@@ -35,7 +35,6 @@ def minimal_config():
             tools_ngs_mapping: ['bwa']
             path_ngs_mapping: ../ngs_mapping
             tools_somatic_variant_calling: ['mutect2']
-            path_somatic_variant_calling: ../somatic_variant_calling
             tools_somatic_variant_annotation: ['jannovar']
             filtration_schema: sets
             filter_sets: {}
@@ -521,7 +520,7 @@ def test_one_filter_step_part_get_input_files(somatic_variant_filtration_workflo
         }
     )
     expected = {
-        "vcf": "somatic_variant_annotation/output/{mapper}.{var_caller}.{annotator}.{tumor_library}/out/{mapper}.{var_caller}.{annotator}.{tumor_library}.vcf.gz",
+        "vcf": "../somatic_variant_annotation/output/{mapper}.{var_caller}.{annotator}.{tumor_library}/out/{mapper}.{var_caller}.{annotator}.{tumor_library}.vcf.gz",
         "bam": "../ngs_mapping/output/{mapper}.{tumor_library}/out/{mapper}.{tumor_library}.bam",
         "normal": "../ngs_mapping/output/{mapper}.P001-N1-DNA1-WGS1/out/{mapper}.P001-N1-DNA1-WGS1.bam",
     }

diff --git a/tests/snappy_pipeline/workflows/test_workflows_variant_filtration.py b/tests/snappy_pipeline/workflows/test_workflows_variant_filtration.py
@@ -42,7 +42,7 @@ def minimal_config():
             gatk3_hc: {}
 
           variant_filtration:
-            path_variant_annotation: VAR_ANNOTATION
+            path_variant_annotation: ../variant_annotation
             tools_ngs_mapping: ['bwa']
             tools_variant_calling: ['gatk3_hc']
             # Testing 1 out 40+ possible combinations:
@@ -104,7 +104,7 @@ def test_filter_quality_step_part_get_input_files(variant_filtration_workflow, p
     )
     # Define expected
     var_base_name = (
-        "VAR_ANNOTATION/output/bwa.gatk3_hc.jannovar_annotate_vcf.P001-N1-DNA1-WGS1/out/"
+        "../variant_annotation/output/bwa.gatk3_hc.jannovar_annotate_vcf.P001-N1-DNA1-WGS1/out/"
         "bwa.gatk3_hc.jannovar_annotate_vcf.P001-N1-DNA1-WGS1"
     )
     pedigree_dict = {