feat: use filtered variants in tmb and signatures (#470)

snappy_pipeline/workflows/somatic_msi_calling/__init__.py

@@ -150,7 +150,7 @@ def get_resource_usage(self, action):
         self._validate_action(action)
         return ResourceUsage(
             threads=3,
-            time="02:00:00",  # 2 hours
+            time="08:00:00",  # 2 hours
             memory=f"{30 * 1024 * 3}M",
         )
 

snappy_pipeline/workflows/somatic_variant_filtration/Snakefile

@@ -159,6 +159,96 @@ rule variant_filtration_filter_to_exons_run:
         wf.wrapper_path("somatic_variant_filtration/filter_to_exons")
 
 
+# Flexible Somatic Variant Filtration ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
+checkpoint one_dkfz:
+    input:
+        unpack(wf.get_input_files("one_dkfz", "run")),
+    output:
+        **wf.get_output_files("one_dkfz", "run"),
+    threads: wf.get_resource("one_dkfz", "run", "threads")
+    resources:
+        time=wf.get_resource("one_dkfz", "run", "time"),
+        memory=wf.get_resource("one_dkfz", "run", "memory"),
+        partition=wf.get_resource("one_dkfz", "run", "partition"),
+        tmpdir=wf.get_resource("one_dkfz", "run", "tmpdir"),
+    log:
+        **wf.get_log_file("one_dkfz", "run"),
+    wrapper:
+        wf.wrapper_path("dkfz_bias_filter")
+
+
+checkpoint one_ebfilter:
+    input:
+        unpack(wf.get_input_files("one_ebfilter", "run")),
+    output:
+        **wf.get_output_files("one_ebfilter", "run"),
+    params:
+        wf.get_params("one_ebfilter", "run"),
+    threads: wf.get_resource("one_ebfilter", "run", "threads")
+    resources:
+        time=wf.get_resource("one_ebfilter", "run", "time"),
+        memory=wf.get_resource("one_ebfilter", "run", "memory"),
+        partition=wf.get_resource("one_ebfilter", "run", "partition"),
+        tmpdir=wf.get_resource("one_ebfilter", "run", "tmpdir"),
+    log:
+        **wf.get_log_file("one_ebfilter", "run"),
+    wrapper:
+        wf.wrapper_path("eb_filter_par")
+
+
+checkpoint one_bcftools:
+    input:
+        unpack(wf.get_input_files("one_bcftools", "run")),
+    output:
+        **wf.get_output_files("one_bcftools", "run"),
+    threads: wf.get_resource("one_bcftools", "run", "threads")
+    resources:
+        time=wf.get_resource("one_bcftools", "run", "time"),
+        memory=wf.get_resource("one_bcftools", "run", "memory"),
+        partition=wf.get_resource("one_bcftools", "run", "partition"),
+        tmpdir=wf.get_resource("one_bcftools", "run", "tmpdir"),
+    log:
+        **wf.get_log_file("one_bcftools", "run"),
+    wrapper:
+        wf.wrapper_path("bcftools/filter")
+
+
+checkpoint one_regions:
+    input:
+        unpack(wf.get_input_files("one_regions", "run")),
+    output:
+        **wf.get_output_files("one_regions", "run"),
+    threads: wf.get_resource("one_regions", "run", "threads")
+    resources:
+        time=wf.get_resource("one_regions", "run", "time"),
+        memory=wf.get_resource("one_regions", "run", "memory"),
+        partition=wf.get_resource("one_regions", "run", "partition"),
+        tmpdir=wf.get_resource("one_regions", "run", "tmpdir"),
+    log:
+        **wf.get_log_file("one_regions", "run"),
+    wrapper:
+        wf.wrapper_path("bcftools/regions")
+
+
+rule last_filter:
+    input:
+        wf.get_input_files("last_filter", "run"),
+    output:
+        **wf.get_output_files("last_filter", "run"),
+    threads: wf.get_resource("last_filter", "run", "threads")
+    resources:
+        time=wf.get_resource("last_filter", "run", "time"),
+        memory=wf.get_resource("last_filter", "run", "memory"),
+        partition=wf.get_resource("last_filter", "run", "partition"),
+        tmpdir=wf.get_resource("last_filter", "run", "tmpdir"),
+    log:
+        **wf.get_log_file("last_filter", "run"),
+    wrapper:
+        wf.wrapper_path("somatic_variant_filtration/apply_all_filters")
+
+
 # Variant Statistics Computation ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # Run Jannovar statistics -----------------------------------------------------
 # TODO