feat: render single sample (#140)

* feat: render single sample * update varlociraptor * fix template * move to rule * Update workflow/rules/common.smk Co-authored-by: Johannes Köster <[email protected]> * adjust function call * snakefmt * typo * fix function call Co-authored-by: Johannes Köster <[email protected]>
snakemake-workflows · May 10, 2022 · 2858ca8 · 2858ca8
1 parent a6cceec
commit 2858ca8
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diff --git a/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml b/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml
@@ -1,6 +1,6 @@
 name: ?f"Variant calls {wildcards.event}"
 
-default-view: overview
+default-view: ?"overview" if input.variant_oncoprints else f"{params.groups[0]}-coding"
 
 __definitions__:
   - |
@@ -55,23 +55,24 @@ __definitions__:
     """
 
 datasets:
-  gene-oncoprint:
-    path: ?params.gene_oncoprint
-    separator: "\t"
-    links:
-      gene details:
-        column: symbol
-        view: "overview-{value}"
-  ?for gene, path in params.variant_oncoprints:
-    ?f"variant-oncoprint-{gene}":
-      path: ?path
+  ?if input.variant_oncoprints:
+    gene-oncoprint:
+      path: ?params.gene_oncoprint
       separator: "\t"
       links:
-        ?for group in params.groups:
-          ?group:
-            column: hgvsp
-            table-row: ?f"{group}-coding/hgvsp"
-            optional: true
+        gene details:
+          column: symbol
+          view: "overview-{value}"
+    ?for gene, path in params.variant_oncoprints:
+      ?f"variant-oncoprint-{gene}":
+        path: ?path
+        separator: "\t"
+        links:
+          ?for group in params.groups:
+            ?group:
+              column: hgvsp
+              table-row: ?f"{group}-coding/hgvsp"
+              optional: true
 
   ?for group, path in zip(params.groups, params.coding_calls):
     ?f"{group}-coding":

diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -836,12 +836,17 @@ def get_oncoprint_input(wildcards):
 
 
 def get_variant_oncoprint_tables(wildcards, input):
-    oncoprint_dir = input.variant_oncoprints
-    valid = re.compile(r"^[^/]+\.tsv$")
-    tables = [f for f in os.listdir(oncoprint_dir) if valid.match(f)]
-    assert all(table.endswith(".tsv") for table in tables)
-    genes = [gene_table[:-4] for gene_table in tables]
-    return list(zip(genes, expand(f"{oncoprint_dir}/{{oncoprint}}", oncoprint=tables)))
+    if input.variant_oncoprints:
+        oncoprint_dir = input.variant_oncoprints
+        valid = re.compile(r"^[^/]+\.tsv$")
+        tables = [f for f in os.listdir(oncoprint_dir) if valid.match(f)]
+        assert all(table.endswith(".tsv") for table in tables)
+        genes = [gene_table[:-4] for gene_table in tables]
+        return list(
+            zip(genes, expand(f"{oncoprint_dir}/{{oncoprint}}", oncoprint=tables))
+        )
+    else:
+        return []
 
 
 def get_datavzrd_report_labels(wildcards):
@@ -886,3 +891,28 @@ def get_fastqc_results(wildcards):
 
     # samtools stats
     yield from expand("results/qc/{sample}.bam.stats", sample=group_samples)
+
+
+def get_variant_oncoprints(wildcards):
+    if len(get_report_batch(wildcards)) > 1:
+        return "results/tables/oncoprints/{wildcards.batch}.{wildcards.event}/variant-oncoprints"
+    else:
+        return []
+
+
+def get_oncoprint(oncoprint_type):
+    def inner(wildcards):
+        if len(get_report_batch(wildcards)) > 1:
+            oncoprint_path = (
+                f"results/tables/oncoprints/{wildcards.batch}.{wildcards.event}"
+            )
+            if oncoprint_type == "gene":
+                return f"{oncoprint_path}/gene-oncoprint.tsv"
+            elif oncoprint_type == "variant":
+                return f"{oncoprint_path}/variant-oncoprints"
+            else:
+                raise ValueError(f"bug: unsupported oncoprint type {oncoprint_type}")
+        else:
+            return []
+
+    return inner
diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk
@@ -42,11 +42,11 @@ rule render_datavzrd_config:
         template=workflow.source_path(
             "../resources/datavzrd/variant-calls-template.datavzrd.yaml"
         ),
-        variant_oncoprints="results/tables/oncoprints/{batch}.{event}/variant-oncoprints",
+        variant_oncoprints=get_oncoprint("variant"),
     output:
         "resources/datavzrd/{batch}.{event}.datavzrd.yaml",
     params:
-        gene_oncoprint="results/tables/oncoprints/{batch}.{event}/gene-oncoprint.tsv",
+        gene_oncoprint=get_oncoprint("gene"),
         variant_oncoprints=get_variant_oncoprint_tables,
         groups=get_report_batch,
         coding_calls=get_datavzrd_data(impact="coding"),