feat: preparation for somatic cnv

snappy_pipeline/apps/snappy_snake.py

@@ -22,6 +22,8 @@
     cbioportal_export,
     gene_expression_quantification,
     gene_expression_report,
+    germline_snvs,
+    guess_sex,
     helper_gcnv_model_targeted,
     helper_gcnv_model_wgs,
     hla_typing,
@@ -41,6 +43,7 @@
     somatic_variant_calling,
     somatic_variant_filtration,
     somatic_variant_signatures,
+    somatic_variants_for_cnv,
     somatic_wgs_cnv_calling,
     somatic_wgs_sv_calling,
     sv_calling_targeted,
@@ -70,9 +73,11 @@
 #: Mapping from step name to module
 STEP_TO_MODULE = {
     "adapter_trimming": adapter_trimming,
+    "cbioportal_export": cbioportal_export,
     "gene_expression_quantification": gene_expression_quantification,
     "gene_expression_report": gene_expression_report,
-    "cbioportal_export": cbioportal_export,
+    "germline_snvs": germline_snvs,
+    "guess_sex": guess_sex,
     "helper_gcnv_model_targeted": helper_gcnv_model_targeted,
     "helper_gcnv_model_wgs": helper_gcnv_model_wgs,
     "hla_typing": hla_typing,
@@ -92,6 +97,7 @@
     "somatic_variant_calling": somatic_variant_calling,
     "somatic_variant_filtration": somatic_variant_filtration,
     "somatic_variant_signatures": somatic_variant_signatures,
+    "somatic_variants_for_cnv": somatic_variants_for_cnv,
     "somatic_wgs_cnv_calling": somatic_wgs_cnv_calling,
     "somatic_wgs_sv_calling": somatic_wgs_sv_calling,
     "sv_calling_targeted": sv_calling_targeted,