Add paper workflow. HEAD paper-2026-workflow main

This workflow is used to compute the results in the paper.

1 files changed, 145 insertions, 0 deletions

diff --git a/paper-2026/benchmark.scm b/paper-2026/benchmark.scm
new file mode 100644
index 0000000..241b41e
--- /dev/null
+++ b/paper-2026/benchmark.scm
@@ -0,0 +1,145 @@
+(define odgi-build
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "${ var prefix='--format={\"metrics\": \"build %e %U %S %M\", \"odgi-graph\": {\"class\": \"File\", \"path\": \"'; var suffix='\"}}'; switch (inputs.tool) { case \"odgi\": return prefix + inputs.graph.nameroot + '.og' + suffix; case \"domagi\": return prefix + inputs.graph.nameroot + '.db' + suffix; }}" "--output=cwl.output.json" tool "build" ("-t" threads) ("-g" graph) ("-o" "${switch (inputs.tool) { case \"odgi\": return inputs.graph.nameroot + \".og\"; case \"domagi\": return inputs.graph.nameroot + \".db\";}}")
+           #:outputs (metrics #:type string) (odgi-graph #:binding ((glob . "${switch (inputs.tool) { case \"odgi\": return inputs.graph.nameroot + \".og\"; case \"domagi\": return inputs.graph.nameroot + \".db\";}}")))
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-paths
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"paths %e %U %S %M\"}" "--output=cwl.output.json" tool "paths" ("-t" threads) ("-i" graph) "--list-paths"
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-crush
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"crush %e %U %S %M\"}" "--output=cwl.output.json" tool "crush" ("-t" threads) ("-i" graph) ("-o" "${switch (inputs.tool) { case \"odgi\": return inputs.graph.nameroot + \".og\"; case \"domagi\": return inputs.graph.nameroot + \".db\";}}")
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-depth
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"depth %e %U %S %M\"}" "--output=cwl.output.json" tool "depth" ("-t" threads) ("-i" graph)
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-depth-graph-depth-table
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"depth-table %e %U %S %M\"}" "--output=cwl.output.json" tool "depth" ("-t" threads) ("-i" graph) "--graph-depth-table"
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-matrix
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"matrix %e %U %S %M\"}" "--output=cwl.output.json" tool "matrix" ("-t" threads) ("-i" graph)
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-stats
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"stats %e %U %S %M\"}" "--output=cwl.output.json" tool "stats" ("-t" threads) ("-i" graph)
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define odgi-view
+  (command #:inputs (tool #:type string) graph (threads #:type int)
+           #:run "time" "--format={\"metrics\": \"view %e %U %S %M\"}" "--output=cwl.output.json" tool "view" ("-t" threads) ("-i" graph) "--to-gfa"
+	   #:outputs (metrics #:type string)
+           #:other ((hints (ResourceRequirement
+                            (coresMin . "$(inputs.threads)"))
+                           (SoftwareRequirement
+                            (packages . #(((package . "domagi"))
+                                          ((package . "odgi"))
+                                          ((package . "time")))))))))
+
+(define combine-metrics
+  (command #:inputs (tool #:type string) (build_metrics #:type string) (crush_metrics #:type string) (depth_metrics #:type string) (depth_graph_depth_table_metrics #:type string) (matrix_metrics #:type string) (paths_metrics #:type string) (stats_metrics #:type string) (view_metrics #:type string)
+           #:run "echo" "$([inputs.build_metrics, inputs.crush_metrics, inputs.depth_metrics, inputs.depth_graph_depth_table_metrics, inputs.matrix_metrics, inputs.paths_metrics, inputs.stats_metrics, inputs.view_metrics].join(`\n`))"
+           #:outputs (metrics #:type stdout)
+           #:stdout "$(inputs.tool)-metrics"
+           #:other ((hints (SoftwareRequirement
+                            (packages . #(((package . "coreutils")))))))))
+
+(define benchmark-tool
+  (workflow ((tool #:type string) chr8 (threads #:type int))
+    (pipe (odgi-build #:tool tool
+                      #:graph chr8
+		      #:threads threads)
+	  (rename #:build-metrics metrics)
+	  (tee (identity)
+               (pipe (odgi-crush #:tool tool
+                                 #:graph odgi-graph
+				 #:threads threads)
+		     (rename #:crush-metrics metrics))
+	       (pipe (odgi-depth #:tool tool
+                                 #:graph odgi-graph
+				 #:threads threads)
+		     (rename #:depth-metrics metrics))
+	       (pipe (odgi-depth-graph-depth-table #:tool tool
+                                                   #:graph odgi-graph
+	        			           #:threads threads)
+	             (rename #:depth-graph-depth-table-metrics metrics))
+               (pipe (odgi-matrix #:tool tool
+                                 #:graph odgi-graph
+				 #:threads threads)
+		     (rename #:matrix-metrics metrics))
+	       (pipe (odgi-paths #:tool tool
+                                 #:graph odgi-graph
+				 #:threads threads)
+		     (rename #:paths-metrics metrics))
+	       (pipe (odgi-stats #:tool tool
+                                 #:graph odgi-graph
+				 #:threads threads)
+		     (rename #:stats-metrics metrics))
+               (pipe (odgi-view #:tool tool
+                                #:graph odgi-graph
+				#:threads threads)
+		     (rename #:view-metrics metrics)))
+          (combine-metrics #:tool tool
+                           #:build_metrics build-metrics
+                           #:crush_metrics crush-metrics
+                           #:depth_metrics depth-metrics
+                           #:depth_graph_depth_table_metrics depth-graph-depth-table-metrics
+                           #:matrix_metrics matrix-metrics
+                           #:paths_metrics paths-metrics
+                           #:stats_metrics stats-metrics
+                           #:view_metrics view-metrics))))
+
+(workflow ((tools #:type (array string)) chr8 (threads #:type int))
+  (scatter (benchmark-tool #:chr8 chr8
+                           #:threads threads)
+           #:tool tools))