diff --git a/tests/snappy_pipeline/workflows/conftest.py b/tests/snappy_pipeline/workflows/conftest.py index 7321e14a1..c7723397c 100644 --- a/tests/snappy_pipeline/workflows/conftest.py +++ b/tests/snappy_pipeline/workflows/conftest.py @@ -604,6 +604,7 @@ def cancer_sheet_tsv(): P002\tT1\tY\tWGS\tP002_T1_DNA1_WGS1\tAgilent SureSelect Human All Exon V6\tDNA P002\tT2\tY\tWGS\tP002_T2_DNA1_WGS1\tAgilent SureSelect Human All Exon V6\tDNA P002\tT2\tY\tmRNA_seq\tP002_T2-RNA1_mRNA_seq1\tNone\tRNA + # P003\tT1\tY\tWGS\tP003_T1_DNA1_WGS1\tNone\tDNA """ ).lstrip() diff --git a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py index a392f1556..3534bc6b1 100644 --- a/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py +++ b/tests/snappy_pipeline/workflows/test_workflows_somatic_variant_filtration.py @@ -521,6 +521,39 @@ def test_one_filter_step_part_get_input_files(somatic_variant_filtration_workflo actual = somatic_variant_filtration_workflow_list.get_input_files("one_dkfz", "run")(wildcards) assert actual == expected + # wildcards = Wildcards( + # fromdict={ + # "mapper": "bwa", + # "var_caller": "mutect2", + # "annotator": "jannovar", + # "tumor_library": "P003-T1-DNA1-WGS1", + # "filter_nb": 1, + # } + # ) + # expected = { + # "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", + # } + # actual = somatic_variant_filtration_workflow_list.get_input_files("one_dkfz", "run")(wildcards) + # assert actual == expected + + wildcards = Wildcards( + fromdict={ + "mapper": "bwa", + "var_caller": "mutect2", + "annotator": "jannovar", + "tumor_library": "P001-T1-DNA1-WGS1", + "filter_nb": 2, + } + ) + expected = { + "vcf": "work/{mapper}.{var_caller}.{annotator}.{tumor_library}/out/{mapper}.{var_caller}.{annotator}.{tumor_library}.dkfz_1.vcf.gz", + } + actual = somatic_variant_filtration_workflow_list.get_input_files("one_bcftools", "run")( + wildcards + ) + assert actual == expected + def test_one_filter_step_part_get_output_files(somatic_variant_filtration_workflow_list): """Tests ApplyFiltersStepPart.get_output_files()"""