broadinstitute/wdltool

graph --all option is unimplemented

Closed this issue · 2 comments

rgobbel commented

The current version of wdltool doesn't appear to implement the --all option. This would be very useful. Any idea when it might be implemented? If it won't be any time soon, the documentation should reflect that.

cjllanwarne commented

This was actually removed because it created enormous and unreadable spaghetti in all but the simplest toy use cases. We should update the docs to remove mention of it.

If you really want to see the internal linkings of your workflow you could either

  • Go back in time to before when it was removed (it looks like it was removed with the addition of womgraph)
  • Check out the wdltool womgraph mode instead, which replaced it with a more rigorous (and perhaps even less readable) format

Either way, I'd warn you that it might sound more useful than it ended up being :)

rgobbel commented

Here's what happens when I try womgraph:

[rgobbel@ussd-prd-rdln02]$ java -jar lib/wdltool-0.14.jar womgraph input_pipeline.wdl Exception in thread "main" java.lang.Exception: Declaration not yet supported in WOM at wdl4s.wdl.WdlCall$.outputPortFromNode(WdlCall.scala:69) at wdl4s.wdl.WdlCall$.$anonfun$buildWomNodeAndInputs$5(WdlCall.scala:56) at scala.Option.map(Option.scala:146) at wdl4s.wdl.WdlCall$.$anonfun$buildWomNodeAndInputs$4(WdlCall.scala:55) at scala.Option.flatMap(Option.scala:171) at wdl4s.wdl.WdlCall$.$anonfun$buildWomNodeAndInputs$3(WdlCall.scala:54) at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:241) at scala.collection.immutable.List.foreach(List.scala:378) at scala.collection.TraversableLike.flatMap(TraversableLike.scala:241) at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:238) at scala.collection.immutable.List.flatMap(List.scala:341) at wdl4s.wdl.WdlCall$.$anonfun$buildWomNodeAndInputs$2(WdlCall.scala:53) at scala.collection.TraversableLike$WithFilter.$anonfun$flatMap$2(TraversableLike.scala:770) at scala.collection.immutable.HashMap$HashMap1.foreach(HashMap.scala:225) at scala.collection.immutable.HashMap$HashTrieMap.foreach(HashMap.scala:432) at scala.collection.TraversableLike$WithFilter.flatMap(TraversableLike.scala:769) at wdl4s.wdl.WdlCall$.wdl4s$wdl$WdlCall$$buildWomNodeAndInputs(WdlCall.scala:52) at wdl4s.wdl.WdlCall.x$4$lzycompute(WdlCall.scala:95) at wdl4s.wdl.WdlCall.x$4(WdlCall.scala:95) at wdl4s.wdl.WdlCall.womInputs$lzycompute(WdlCall.scala:95) at wdl4s.wdl.WdlCall.womInputs(WdlCall.scala:95) at wdl4s.wdl.WdlCall.womGraphInputNodes$lzycompute(WdlCall.scala:99) at wdl4s.wdl.WdlCall.womGraphInputNodes(WdlCall.scala:99) at wdl4s.wdl.WdlWorkflow$.$anonfun$buildWomGraph$1(WdlWorkflow.scala:54) at scala.collection.TraversableOnce.$anonfun$foldLeft$1(TraversableOnce.scala:157) at scala.collection.TraversableOnce.$anonfun$foldLeft$1$adapted(TraversableOnce.scala:157) at scala.collection.immutable.HashSet$HashSet1.foreach(HashSet.scala:320) at scala.collection.immutable.HashSet$HashTrieSet.foreach(HashSet.scala:976) at scala.collection.TraversableOnce.foldLeft(TraversableOnce.scala:157) at scala.collection.TraversableOnce.foldLeft$(TraversableOnce.scala:155) at scala.collection.AbstractTraversable.foldLeft(Traversable.scala:104) at wdl4s.wdl.WdlWorkflow$.buildWomGraph(WdlWorkflow.scala:53) at wdl4s.wdl.WdlWorkflow$.womWorkflowDefinition(WdlWorkflow.scala:69) at wdl4s.wdl.WdlWorkflow.womDefinition$lzycompute(WdlWorkflow.scala:86) at wdl4s.wdl.WdlWorkflow.womDefinition(WdlWorkflow.scala:86) at wdl4s.wdl.WdlNamespaceWithWorkflow.womExecutable$lzycompute(WdlNamespace.scala:76) at wdl4s.wdl.WdlNamespaceWithWorkflow.womExecutable(WdlNamespace.scala:76) at wdltool.graph.WomGraphPrint$.womExecutableFromWdl(WomGraphPrint.scala:27) at wdltool.graph.WomGraphPrint$.generateWorkflowDigraph(WomGraphPrint.scala:51) at wdltool.Main$.$anonfun$womGraph$2(Main.scala:100) at wdltool.Main$.continueIf(Main.scala:112) at wdltool.Main$.womGraph(Main.scala:96) at wdltool.Main$.dispatchCommand(Main.scala:38) at wdltool.Main$.delayedEndpoint$wdltool$Main$1(Main.scala:176) at wdltool.Main$delayedInit$body.apply(Main.scala:12) at scala.Function0.apply$mcV$sp(Function0.scala:34) at scala.Function0.apply$mcV$sp$(Function0.scala:34) at scala.runtime.AbstractFunction0.apply$mcV$sp(AbstractFunction0.scala:12) at scala.App.$anonfun$main$1$adapted(App.scala:76) at scala.collection.immutable.List.foreach(List.scala:378) at scala.App.main(App.scala:76) at scala.App.main$(App.scala:74) at wdltool.Main$.main(Main.scala:12) at wdltool.Main.main(Main.scala)