fix: use latest datavzrd wrapper, integrating templating of config, t…

…hereby avoiding leaks of local storage paths into datavzrd config (#74) * fix: group render and report rules together in order to avoid leaks of local storage paths into datavzrd config Otherwise, the consuming rule can fail on certain systems where local storage paths are job specific * fix: snakefmt * use latest wrapper, omitting the grouping stuff entirely * use yte --------- Co-authored-by: Famke Bäuerle <[email protected]>
snakemake-workflows · May 4, 2024 · 40a64ed · 40a64ed
1 parent 65930c5
commit 40a64ed
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 35 deletions.
diff --git a/workflow/resources/datavzrd/fp-fn-config.yte.yaml b/workflow/resources/datavzrd/fp-fn-config.yte.yaml
@@ -1,3 +1,5 @@
+__use_yte__: true
+
 __definitions__:
   - import os
   - import pandas as pd

diff --git a/workflow/resources/datavzrd/precision-recall-config.yte.yaml b/workflow/resources/datavzrd/precision-recall-config.yte.yaml
@@ -1,3 +1,5 @@
+__use_yte__: true
+
 __variables__:
   green: "#74c476"
   orange: "#fd8d3c"
@@ -9,7 +11,7 @@ default-view: results-table
 
 datasets:
   results:
-    path: ?input.dataset
+    path: ?input.table
     separator: "\t"
     links:
       link to table:

diff --git a/workflow/rules/eval.smk b/workflow/rules/eval.smk
@@ -242,25 +242,11 @@ rule collect_precision_recall:
         "../scripts/collect-precision-recall.py"
 
 
-rule render_precision_recall_report_config:
+rule report_precision_recall:
     input:
-        dataset="results/precision-recall/benchmarks/{benchmark}.{vartype}.tsv",
-        template=workflow.source_path(
+        config=workflow.source_path(
             "../resources/datavzrd/precision-recall-config.yte.yaml"
         ),
-    params:
-        somatic=get_somatic_status,
-    output:
-        "results/datavzrd-config/precision-recall/{benchmark}/{vartype}.config.yaml",
-    log:
-        "logs/yte/datavzrd-config/precision-recall/{benchmark}/{vartype}.log",
-    template_engine:
-        "yte"
-
-
-rule report_precision_recall:
-    input:
-        config="results/datavzrd-config/precision-recall/{benchmark}/{vartype}.config.yaml",
         table="results/precision-recall/benchmarks/{benchmark}.{vartype}.tsv",
     output:
         report(
@@ -271,8 +257,10 @@ rule report_precision_recall:
         ),
     log:
         "logs/datavzrd/precision-recall/{benchmark}/{vartype}.log",
+    params:
+        somatic=get_somatic_status,
     wrapper:
-        "v2.13.0/utils/datavzrd"
+        "v3.10.1/utils/datavzrd"
 
 
 rule extract_fp_fn:
@@ -316,26 +304,11 @@ rule collect_fp_fn:
         "../scripts/collect-fp-fn.py"
 
 
-rule render_fp_fn_report_config:
-    input:
-        main_dataset="results/fp-fn/genomes/{genome}/{cov}/{classification}/main.tsv",
-        dependency_sorting_datasets="results/fp-fn/genomes/{genome}/{cov}/{classification}/dependency-sorting",
-        template=workflow.source_path("../resources/datavzrd/fp-fn-config.yte.yaml"),
-    output:
-        "results/datavzrd-config/fp-fn/{genome}/{cov}/{classification}.config.yaml",
-    params:
-        labels=lambda w: get_callsets_labels(get_genome_callsets(w.genome)),
-    log:
-        "logs/yte/datavzrd-config/fp-fn/{genome}/{cov}/{classification}.log",
-    template_engine:
-        "yte"
-
-
 rule report_fp_fn:
     input:
         main_dataset="results/fp-fn/genomes/{genome}/{cov}/{classification}/main.tsv",
         dependency_sorting_datasets="results/fp-fn/genomes/{genome}/{cov}/{classification}/dependency-sorting",
-        config="results/datavzrd-config/fp-fn/{genome}/{cov}/{classification}.config.yaml",
+        config=workflow.source_path("../resources/datavzrd/fp-fn-config.yte.yaml"),
     output:
         report(
             directory("results/report/fp-fn/{genome}/{cov}/{classification}"),
@@ -346,5 +319,7 @@ rule report_fp_fn:
         ),
     log:
         "logs/datavzrd/fp-fn/{genome}/{cov}/{classification}.log",
+    params:
+        labels=lambda w: get_callsets_labels(get_genome_callsets(w.genome)),
     wrapper:
-        "v2.13.0/utils/datavzrd"
+        "v3.10.1/utils/datavzrd"