feat: change varfish-annotator to mehari (#392) (#393)

snappy_pipeline/workflows/varfish_export/Snakefile

@@ -45,67 +45,67 @@ rule varfish_export_write_pedigree_run:
         wf.substep_dispatch("write_pedigree", "run", wildcards, output)
 
 
-# Run varfish-annotator-cli annotate ------------------------------------------
+# Run varfish-annotator-cli annotate-seqvars -----------------------------------
 
 
-rule varfish_export_varfish_annotator_annotate:
+rule varfish_export_mehari_annotate_seqvars:
     input:
-        unpack(wf.get_input_files("varfish_annotator", "annotate")),
+        unpack(wf.get_input_files("mehari", "annotate_seqvars")),
     output:
-        **wf.get_output_files("varfish_annotator", "annotate"),
-    threads: wf.get_resource("varfish_annotator", "annotate", "threads")
+        **wf.get_output_files("mehari", "annotate_seqvars"),
+    threads: wf.get_resource("mehari", "annotate_seqvars", "threads")
     resources:
-        time=wf.get_resource("varfish_annotator", "annotate", "time"),
-        memory=wf.get_resource("varfish_annotator", "annotate", "memory"),
-        partition=wf.get_resource("varfish_annotator", "annotate", "partition"),
-        tmpdir=wf.get_resource("varfish_annotator", "annotate", "tmpdir"),
+        time=wf.get_resource("mehari", "annotate_seqvars", "time"),
+        memory=wf.get_resource("mehari", "annotate_seqvars", "memory"),
+        partition=wf.get_resource("mehari", "annotate_seqvars", "partition"),
+        tmpdir=wf.get_resource("mehari", "annotate_seqvars", "tmpdir"),
     log:
-        **wf.get_log_file("varfish_annotator", "annotate"),
+        **wf.get_log_file("mehari", "annotate_seqvars"),
     params:
-        **{"args": wf.get_params("varfish_annotator", "annotate")},
+        **{"args": wf.get_params("mehari", "annotate_seqvars")},
     wrapper:
-        wf.wrapper_path("varfish_annotator/annotate")
+        wf.wrapper_path("mehari/annotate_seqvars")
 
 
-# Run varfish-annotator-cli annotate-svs ---------------------------------------
+# Run varfish-annotator-cli annotate-strucvars ---------------------------------
 
 
-rule varfish_export_varfish_annotator_annotate_svs:
+rule varfish_export_mehari_annotate_strucvars:
     input:
-        unpack(wf.get_input_files("varfish_annotator", "annotate_svs")),
+        unpack(wf.get_input_files("mehari", "annotate_strucvars")),
     output:
-        **wf.get_output_files("varfish_annotator", "annotate_svs"),
-    threads: wf.get_resource("varfish_annotator", "annotate_svs", "threads")
+        **wf.get_output_files("mehari", "annotate_strucvars"),
+    threads: wf.get_resource("mehari", "annotate_strucvars", "threads")
     resources:
-        time=wf.get_resource("varfish_annotator", "annotate_svs", "time"),
-        memory=wf.get_resource("varfish_annotator", "annotate_svs", "memory"),
-        partition=wf.get_resource("varfish_annotator", "annotate_svs", "partition"),
-        tmpdir=wf.get_resource("varfish_annotator", "annotate_svs", "tmpdir"),
+        time=wf.get_resource("mehari", "annotate_strucvars", "time"),
+        memory=wf.get_resource("mehari", "annotate_strucvars", "memory"),
+        partition=wf.get_resource("mehari", "annotate_strucvars", "partition"),
+        tmpdir=wf.get_resource("mehari", "annotate_strucvars", "tmpdir"),
     log:
-        **wf.get_log_file("varfish_annotator", "annotate_svs"),
+        **wf.get_log_file("mehari", "annotate_strucvars"),
     params:
-        **{"args": wf.get_params("varfish_annotator", "annotate_svs")},
+        **{"args": wf.get_params("mehari", "annotate_strucvars")},
     wrapper:
-        wf.wrapper_path("varfish_annotator/annotate_svs")
+        wf.wrapper_path("mehari/annotate_strucvars")
 
 
 # Gather statistics about the alignment ---------------------------------------
 
 
-rule varfish_export_varfish_annotator_bam_qc:
+rule varfish_export_mehari_bam_qc:
     input:
-        unpack(wf.get_input_files("varfish_annotator", "bam_qc")),
+        unpack(wf.get_input_files("mehari", "bam_qc")),
     output:
-        **wf.get_output_files("varfish_annotator", "bam_qc"),
-    threads: wf.get_resource("varfish_annotator", "bam_qc", "threads")
+        **wf.get_output_files("mehari", "bam_qc"),
+    threads: wf.get_resource("mehari", "bam_qc", "threads")
     resources:
-        time=wf.get_resource("varfish_annotator", "bam_qc", "time"),
-        memory=wf.get_resource("varfish_annotator", "bam_qc", "memory"),
-        partition=wf.get_resource("varfish_annotator", "bam_qc", "partition"),
-        tmpdir=wf.get_resource("varfish_annotator", "bam_qc", "tmpdir"),
+        time=wf.get_resource("mehari", "bam_qc", "time"),
+        memory=wf.get_resource("mehari", "bam_qc", "memory"),
+        partition=wf.get_resource("mehari", "bam_qc", "partition"),
+        tmpdir=wf.get_resource("mehari", "bam_qc", "tmpdir"),
     log:
-        **wf.get_log_file("varfish_annotator", "bam_qc"),
+        **wf.get_log_file("mehari", "bam_qc"),
     params:
-        **{"args": wf.get_params("varfish_annotator", "bam_qc")},
+        **{"args": wf.get_params("mehari", "bam_qc")},
     wrapper:
-        wf.wrapper_path("varfish_annotator/bam_qc")
+        wf.wrapper_path("mehari/bam_qc")

snappy_pipeline/workflows/varfish_export/__init__.py

@@ -121,26 +121,19 @@
     release: GRCh37              # REQUIRED: default 'GRCh37'
     # Path to BED file with exons; used for reducing data to near-exon small variants.
     path_exon_bed: null          # REQUIRED: exon BED file to use
-    # Path to Jannovar RefSeq ``.ser`` file for annotation
-    path_refseq_ser: REQUIRED    # REQUIRED: path to RefSeq .ser file
-    # Path to Jannovar ENSEMBL ``.ser`` file for annotation
-    path_ensembl_ser: REQUIRED   # REQUIRED: path to ENSEMBL .ser file
-    # Path to VarFish annotator database file to use for annotating.
-    path_db: REQUIRED            # REQUIRED: spath to varfish-annotator DB file to use
+    # Path to mehari database.
+    path_mehari_db: REQUIRED     # REQUIRED: path to mehari database
 """
 
 
-class VarfishAnnotatorAnnotateStepPart(VariantCallingGetLogFileMixin, BaseStepPart):
-    """This step part is responsible for annotating the variants with VarFish Annotator"""
+class MehariStepPart(VariantCallingGetLogFileMixin, BaseStepPart):
+    """This step part is responsible for annotating the variants with Mehari"""
 
-    name = "varfish_annotator"
-    actions = ("annotate", "annotate_svs", "bam_qc")
+    name = "mehari"
+    actions = ("annotate_seqvars", "annotate_strucvars", "bam_qc")
 
     def __init__(self, parent):
         super().__init__(parent)
-        self.base_path_out = (
-            "work/{mapper}.{var_caller}.varfish_annotated.{index_ngs_library}/out/.done"
-        )
         # Build shortcut from index library name to pedigree
         self.index_ngs_library_to_pedigree = {}
         for sheet in self.parent.shortcut_sheets:
@@ -159,7 +152,7 @@ def get_log_file(self, action: str) -> SnakemakeDictItemsGenerator:
         self._validate_action(action)
         prefix = (
             "work/{mapper}.varfish_export.{index_ngs_library}/log/"
-            f"{{mapper}}.varfish_annotator_{action}.{{index_ngs_library}}"
+            f"{{mapper}}.mehari_{action}.{{index_ngs_library}}"
         )
         key_ext = (
             ("wrapper", ".wrapper.py"),
@@ -187,16 +180,16 @@ def get_resource_usage(self, action: str) -> ResourceUsage:
     @listify
     def get_result_files(self, action):
         # Generate templates to the output paths from action's result files.
-        if action == "annotate":
-            raw_path_tpls = self._get_output_files_annotate().values()
-        elif action == "annotate_svs":
-            # Only annotate SVs if path to step for calling them is configured.
+        if action == "annotate_seqvars":
+            raw_path_tpls = self._get_output_files_annotate_seqvars().values()
+        elif action == "annotate_strucvars":
+            # Only annotate_seqvars SVs if path to step for calling them is configured.
             if (
                 not self.parent.config["path_sv_calling_targeted"]
                 and not self.parent.config["path_sv_calling_wgs"]
             ):
                 return
-            raw_path_tpls = self._get_output_files_annotate_svs().values()
+            raw_path_tpls = self._get_output_files_annotate_strucvars().values()
         elif action == "bam_qc":
             raw_path_tpls = self._get_output_files_bam_qc().values()
         # Filter the templates to the paths in the output directory.
@@ -205,7 +198,8 @@ def get_result_files(self, action):
         # Create concrete paths for all pedigrees in the sample sheet.
         index_ngs_libraries = self._get_index_ngs_libraries(
             require_consistent_pedigree_kits=(
-                bool(self.parent.config["path_sv_calling_targeted"]) and (action == "annotate_svs")
+                bool(self.parent.config["path_sv_calling_targeted"])
+                and (action == "annotate_strucvars")
             )
         )
         kwargs = {
@@ -249,7 +243,7 @@ def _is_pedigree_good(self, pedigree: Pedigree) -> bool:
         return not msg
 
     @dictify
-    def _get_input_files_annotate(self, wildcards):
+    def _get_input_files_annotate_seqvars(self, wildcards):
         yield "ped", "work/write_pedigree.{index_ngs_library}/out/{index_ngs_library}.ped"
 
         variant_calling = self.parent.sub_workflows["variant_calling"]
@@ -271,13 +265,13 @@ def _get_input_files_annotate(self, wildcards):
         yield "vcf", vcfs
 
     @dictify
-    def _get_output_files_annotate(self):
+    def _get_output_files_annotate_seqvars(self):
         # Generate paths in "work/" directory
         prefix = (
             "work/{mapper}.varfish_export.{index_ngs_library}/out/"
-            "{mapper}.varfish_annotator_annotate.{index_ngs_library}"
+            "{mapper}.mehari_annotate_seqvars.{index_ngs_library}"
         )
-        work_paths = {  # annotate will write out PED file
+        work_paths = {  # annotate_seqvars will write out PED file
             "ped": f"{prefix}.ped",
             "ped_md5": f"{prefix}.ped.md5",
             "gts": f"{prefix}.gts.tsv.gz",
@@ -289,10 +283,12 @@ def _get_output_files_annotate(self):
         # Generate paths in "output/" directory
         yield "output_links", [
             re.sub(r"^work/", "output/", work_path)
-            for work_path in chain(work_paths.values(), self.get_log_file("annotate").values())
+            for work_path in chain(
+                work_paths.values(), self.get_log_file("annotate_seqvars").values()
+            )
         ]
 
-    def _get_params_annotate(self, wildcards: Wildcards) -> typing.Dict[str, typing.Any]:
+    def _get_params_annotate_seqvars(self, wildcards: Wildcards) -> typing.Dict[str, typing.Any]:
         pedigree = self.index_ngs_library_to_pedigree[wildcards.index_ngs_library]
         for donor in pedigree.donors:
             if (
@@ -303,7 +299,7 @@ def _get_params_annotate(self, wildcards: Wildcards) -> typing.Dict[str, typing.
         return {"step_name": "varfish_export"}
 
     @dictify
-    def _get_input_files_annotate_svs(self, wildcards):
+    def _get_input_files_annotate_strucvars(self, wildcards):
         yield "ped", "work/write_pedigree.{index_ngs_library}/out/{index_ngs_library}.ped"
 
         if self.parent.config["path_sv_calling_targeted"]:
@@ -387,28 +383,28 @@ def _get_input_files_annotate_svs(self, wildcards):
         yield "vcf_cov", cov_vcfs
 
     @dictify
-    def _get_output_files_annotate_svs(self):
+    def _get_output_files_annotate_strucvars(self):
         prefix = (
             "work/{mapper}.varfish_export.{index_ngs_library}/out/"
-            "{mapper}.varfish_annotator_annotate_svs.{index_ngs_library}"
+            "{mapper}.mehari_annotate_strucvars.{index_ngs_library}"
         )
         work_paths = {
             "gts": f"{prefix}.gts.tsv.gz",
             "gts_md5": f"{prefix}.gts.tsv.gz.md5",
-            "feature_effects": f"{prefix}.feature-effects.tsv.gz",
-            "feature_effects_md5": f"{prefix}.feature-effects.tsv.gz.md5",
             "db_infos": f"{prefix}.db-infos.tsv.gz",
             "db_infos_md5": f"{prefix}.db-infos.tsv.gz.md5",
         }
         yield from work_paths.items()
         # Generate paths in "output/" directory
         yield "output_links", [
             re.sub(r"^work/", "output/", work_path)
-            for work_path in chain(work_paths.values(), self.get_log_file("annotate_svs").values())
+            for work_path in chain(
+                work_paths.values(), self.get_log_file("annotate_strucvars").values()
+            )
         ]
 
     #: Alias the get params function.
-    _get_params_annotate_svs = _get_params_annotate
+    _get_params_annotate_strucvars = _get_params_annotate_seqvars
 
     @dictify
     def _get_input_files_bam_qc(self, wildcards):
@@ -439,7 +435,7 @@ def _get_input_files_bam_qc(self, wildcards):
     def _get_output_files_bam_qc(self) -> SnakemakeDictItemsGenerator:
         prefix = (
             "work/{mapper}.varfish_export.{index_ngs_library}/out/"
-            "{mapper}.varfish_annotator_bam_qc.{index_ngs_library}"
+            "{mapper}.mehari_bam_qc.{index_ngs_library}"
         )
         work_paths = {
             "bam_qc": f"{prefix}.bam-qc.tsv.gz",
@@ -502,9 +498,7 @@ def __init__(self, workflow, config, config_lookup_paths, config_paths, workdir)
         )
 
         # Register sub step classes so the sub steps are available
-        self.register_sub_step_classes(
-            (WritePedigreeStepPart, VarfishAnnotatorAnnotateStepPart, LinkOutStepPart)
-        )
+        self.register_sub_step_classes((WritePedigreeStepPart, MehariStepPart, LinkOutStepPart))
 
         # Register sub workflows
         self.register_sub_workflow("variant_calling", self.config["path_variant_calling"])
@@ -564,8 +558,8 @@ def get_result_files(self):
 
         We will process all primary DNA libraries and perform joint calling within pedigrees
         """
-        for action in self.sub_steps["varfish_annotator"].actions:
-            yield from self.sub_steps["varfish_annotator"].get_result_files(action)
+        for action in self.sub_steps["mehari"].actions:
+            yield from self.sub_steps["mehari"].get_result_files(action)
 
     def check_config(self):
         self.ensure_w_config(

snappy_wrappers/wrappers/mehari/annotate_seqvars/environment.yaml

@@ -0,0 +1 @@
+../environment.yaml