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(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))
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