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An implementation of Nextflow.io with Language Workbench Technology. The project helps create computational pipelines that run with the Nextflow.io middleware. Includes dockerfile language and IDE-like support for docker.

Home Page: http://campagnelab.org/software/nextflow-workbench/

License: Other

Shell 24.22% Java 75.78%

nextflowworkbench's Introduction

The Nextflow workbench is a set of languages developed with the Jetbrains MPS Language Workbench that make it easier to write data analysis workflows with Nextflow.

The Nextflow Workbench has several features that complement the Nextflow middleware:

  • It enables the reuse and composition of Nextflow processes across workflows.
  • It provides a custom typesystem that detects incompatible type assignments and reports them directly in the editor.
  • It provides seamless language composition as an effective extension and customization mechanism.
  • It provides a WYSIWYG editor to write analysis workflows meant to be deployed in docker containers (this feature was introduced in feature 1.2).
  • It provides a WYSIWYG editor to create docker images (since 1.2) and to declare which set of popular bioinformatics tools and genome indices should be pre-installed in each image (this feature will be introduced in release 1.3).

See http://campagnelab.org/software/nextflow-workbench/ for details about this project.

Join the chat at https://gitter.im/CampagneLaboratory/NextflowWorkbench

nextflowworkbench's People

Contributors

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Watchers

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Forkers

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nextflowworkbench's Issues

IllegalModelAccessError when trying to run workflow

I moved some of the samples into a writeable model and adjusted to run. The model includes a logger I found in the sample.
jetbrains.mps.smodel.IllegalModelAccessError: You can write model only inside write actions
at jetbrains.mps.smodel.ModelAccess.checkWriteAccess(ModelAccess.java:115)
at jetbrains.mps.smodel.ModelAccessBase.checkWriteAccess(ModelAccessBase.java:48)
at jetbrains.mps.smodel.AttachedNodeOwner.assertLegalChange(AttachedNodeOwner.java:81)
at jetbrains.mps.smodel.SNode.assertCanChange(SNode.java:109)
at jetbrains.mps.smodel.SNode.insertChildBefore(SNode.java:751)
at jetbrains.mps.smodel.SNode.addChild(SNode.java:799)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList$ChildrenSNodesList.doAddReference(AbstractSNodeList.java:163)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList.addReference(AbstractSNodeList.java:38)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList.add(AbstractSNodeList.java:140)
at jetbrains.mps.lang.smodel.generator.smodelAdapter.AbstractSNodeList$ChildrenSNodesList.add(AbstractSNodeList.java:150)
at jetbrains.mps.internal.collections.runtime.AbstractCollectionSequence.addElement(AbstractCollectionSequence.java:20)
at org.campagnelab.logger.behavior.Logger__BehaviorDescriptor.add_id1EUvP1fLbE6(Unknown Source)
at org.campagnelab.logger.behavior.Logger__BehaviorDescriptor.invokeSpecial0(Unknown Source)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeSpecial(BaseBHDescriptor.java:346)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeNonVirtualCommon(BaseBHDescriptor.java:294)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeNonVirtual(BaseBHDescriptor.java:270)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invoke(BaseBHDescriptor.java:231)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke0(SMethodImpl.java:151)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke(SMethodImpl.java:126)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.log(ExecuteDockerCommands.java:655)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.executeLsWithCache(ExecuteDockerCommands.java:731)
at org.campagnelab.docker.bash.behavior.DockerPath__BehaviorDescriptor.doesPathExist_id2h_fDmyfOCy(DockerPath__BehaviorDescriptor.java:126)
at org.campagnelab.docker.bash.behavior.DockerPath__BehaviorDescriptor.invokeSpecial0(DockerPath__BehaviorDescriptor.java:194)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeSpecial(BaseBHDescriptor.java:346)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeVirtual(BaseBHDescriptor.java:305)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invoke(BaseBHDescriptor.java:229)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke0(SMethodImpl.java:151)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke(SMethodImpl.java:126)
at org.campagnelab.docker.bash.typesystem.FileDoesNotExist_NonTypesystemRule.applyRule(FileDoesNotExist_NonTypesystemRule.java:21)
at jetbrains.mps.newTypesystem.context.typechecking.IncrementalTypechecking.applyRuleToNode(IncrementalTypechecking.java:151)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent$3.run(NonTypeSystemComponent.java:343)
at jetbrains.mps.newTypesystem.context.typechecking.IncrementalTypechecking.runApplyRulesTo(IncrementalTypechecking.java:163)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.applyNonTypesystemRulesToNode(NonTypeSystemComponent.java:323)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.applyRulesToRoot(NonTypeSystemComponent.java:312)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.access$000(NonTypeSystemComponent.java:41)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent$2.compute(NonTypeSystemComponent.java:295)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent$2.compute(NonTypeSystemComponent.java:292)
at jetbrains.mps.languageScope.LanguageScopeExecutor.execWithModelScope(LanguageScopeExecutor.java:35)
at jetbrains.mps.newTypesystem.context.component.NonTypeSystemComponent.applyNonTypeSystemRulesToRoot(NonTypeSystemComponent.java:292)
at jetbrains.mps.newTypesystem.context.typechecking.IncrementalTypechecking.applyNonTypesystemRulesToRoot(IncrementalTypechecking.java:231)
at jetbrains.mps.newTypesystem.context.typechecking.BaseTypechecking.applyNonTypesystemRulesToRoot(BaseTypechecking.java:140)
at jetbrains.mps.newTypesystem.context.IncrementalTypecheckingContext.applyNonTypesystemRules(IncrementalTypecheckingContext.java:197)
at jetbrains.mps.newTypesystem.context.SimpleTypecheckingContext.checkRootAndGetErrors(SimpleTypecheckingContext.java:261)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker$1.run(TypesystemChecker.java:34)
at jetbrains.mps.typesystem.inference.TypeContextManager$Executor.doExecute(TypeContextManager.java:266)
at jetbrains.mps.typesystem.inference.TypeContextManager$Executor.execute(TypeContextManager.java:243)
at jetbrains.mps.typesystem.inference.TypeContextManager.runTypeCheckingAction(TypeContextManager.java:118)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker.getErrors(TypesystemChecker.java:32)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker.check(TypesystemChecker.java:45)
at jetbrains.mps.typesystemEngine.checker.TypesystemChecker.check(TypesystemChecker.java:26)
at jetbrains.mps.checkers.IteratingChecker.check(IteratingChecker.java:86)
at jetbrains.mps.checkers.IChecker$AbstractModelChecker$2.check(IChecker.java:63)
at jetbrains.mps.checkers.IChecker$AbstractModelChecker$2.check(IChecker.java:53)
at jetbrains.mps.checkers.CategoryShowingChecker.check(CategoryShowingChecker.java:39)
at jetbrains.mps.checkers.FilteringChecker.check(FilteringChecker.java:27)
at jetbrains.mps.checkers.CatchingChecker.check(CatchingChecker.java:25)
at jetbrains.mps.checkers.AggregatingChecker.check(AggregatingChecker.java:26)
at jetbrains.mps.checkers.SkippingChecker.check(SkippingChecker.java:21)
at jetbrains.mps.checkers.ModelCheckerBuilder$1.check(ModelCheckerBuilder.java:142)
at jetbrains.mps.checkers.ModelCheckerBuilder$1.check(ModelCheckerBuilder.java:114)
at jetbrains.mps.ide.modelchecker.platform.actions.ModelCheckerIssueFinder$1.compute(ModelCheckerIssueFinder.java:62)
at jetbrains.mps.ide.modelchecker.platform.actions.ModelCheckerIssueFinder$1.compute(ModelCheckerIssueFinder.java:54)
at jetbrains.mps.util.ComputeRunnable.compute(ComputeRunnable.java:32)
at jetbrains.mps.util.AbstractComputeRunnable.run(AbstractComputeRunnable.java:27)
at jetbrains.mps.smodel.WorkbenchModelAccess.lambda$runReadAction$0(WorkbenchModelAccess.java:77)
at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:902)
at jetbrains.mps.smodel.WorkbenchModelAccess.runReadAction(WorkbenchModelAccess.java:74)
at jetbrains.mps.smodel.ModelAccessBase.runReadAction(ModelAccessBase.java:53)
at jetbrains.mps.smodel.ModelAccessHelper.runReadAction(ModelAccessHelper.java:44)
at jetbrains.mps.ide.modelchecker.platform.actions.ModelCheckerIssueFinder.execute(ModelCheckerIssueFinder.java:54)
at jetbrains.mps.ide.findusages.view.UsagesView$RerunAction$1.run(UsagesView.java:332)
at com.intellij.openapi.progress.impl.CoreProgressManager$TaskRunnable.run(CoreProgressManager.java:750)
at com.intellij.openapi.progress.impl.CoreProgressManager$5.run(CoreProgressManager.java:434)
at com.intellij.openapi.progress.impl.CoreProgressManager.lambda$runProcess$1(CoreProgressManager.java:157)
at com.intellij.openapi.progress.impl.CoreProgressManager.registerIndicatorAndRun(CoreProgressManager.java:580)
at com.intellij.openapi.progress.impl.CoreProgressManager.executeProcessUnderProgress(CoreProgressManager.java:525)
at com.intellij.openapi.progress.impl.ProgressManagerImpl.executeProcessUnderProgress(ProgressManagerImpl.java:85)
at com.intellij.openapi.progress.impl.CoreProgressManager.runProcess(CoreProgressManager.java:144)
at com.intellij.openapi.application.impl.ApplicationImpl.lambda$null$10(ApplicationImpl.java:565)
at com.intellij.openapi.application.impl.ApplicationImpl$1.run(ApplicationImpl.java:305)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

docker native has been released

Now that docker native has been released we can release the latest changes in NW required for compatibility with this version.

Plugin for MPS 2017

I would love to give Nextflow Workbench a try, but the installation instructions no longer work, and it looks like the latest version of the plugin is not compatible with the current release. Do you intend to update the plugin?

Run the test script

Hi,

I tried to run the example from the tutorial but I can not start it.

You see here the configuration:
nextflow

The MPS IDE reports the following nullpointer exception:

[1918549]  ERROR - llij.ide.plugins.PluginManager - null 
java.lang.NullPointerException
    at org.campagnelab.workflow.run.plugin.NextFlow_RunParameters_Configuration$1.run(Unknown Source)
    at jetbrains.mps.ide.smodel.WorkbenchModelAccess$2.run(WorkbenchModelAccess.java:118)
    at com.intellij.openapi.application.impl.ApplicationImpl.runReadAction(ApplicationImpl.java:896)
    at jetbrains.mps.ide.smodel.WorkbenchModelAccess.runReadAction(WorkbenchModelAccess.java:113)
    at jetbrains.mps.smodel.ModelAccessBase.runReadAction(ModelAccessBase.java:52)
    at org.campagnelab.workflow.run.plugin.NextFlow_RunParameters_Configuration.getAdditionalLibPath(Unknown Source)
    at org.campagnelab.workflow.run.plugin.NextFlow_Configuration_RunProfileState.execute(Unknown Source)
    at com.intellij.execution.runners.DefaultProgramRunner.doExecute(DefaultProgramRunner.java:33)
    at com.intellij.execution.runners.GenericProgramRunner$1.execute(GenericProgramRunner.java:43)
    at com.intellij.execution.RunProfileStarter.execute(RunProfileStarter.java:39)
    at com.intellij.execution.impl.ExecutionManagerImpl$2.run(ExecutionManagerImpl.java:203)
    at com.intellij.openapi.project.DumbServiceImpl.runWhenSmart(DumbServiceImpl.java:125)
    at com.intellij.execution.impl.ExecutionManagerImpl$1$1.run(ExecutionManagerImpl.java:168)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:748)
    at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:577)
    at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:384)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

NPE when trying to build a docker image

Clicking on the Build image button yields this exception (tested in 2018.1.1 with version 1.8.0 of the NW plugin):
null
java.lang.NullPointerException
at jetbrains.mps.lang.smodel.generator.smodelAdapter.SModelOperations.getModuleStub(SModelOperations.java:128)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.getMessageViewTool(ExecuteDockerCommands.java:675)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.log(ExecuteDockerCommands.java:648)
at org.campagnelab.docker.behavior.ExecuteDockerCommands.build(ExecuteDockerCommands.java:553)
at org.campagnelab.docker.behavior.Dockerfile__BehaviorDescriptor.build_id5BbChSjHB1p(Dockerfile__BehaviorDescriptor.java:67)
at org.campagnelab.docker.behavior.Dockerfile__BehaviorDescriptor.invokeSpecial0(Dockerfile__BehaviorDescriptor.java:117)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeSpecial(BaseBHDescriptor.java:346)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeNonVirtualCommon(BaseBHDescriptor.java:294)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invokeNonVirtual(BaseBHDescriptor.java:270)
at jetbrains.mps.core.aspects.behaviour.BaseBHDescriptor.invoke(BaseBHDescriptor.java:231)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke0(SMethodImpl.java:151)
at jetbrains.mps.core.aspects.behaviour.SMethodImpl.invoke(SMethodImpl.java:126)
at org.campagnelab.docker.editor.Dockerfile_EditorBuilder_a$1.process(Dockerfile_EditorBuilder_a.java:126)
at org.campagnelab.ui.code.Swing.ButtonCallback.run(Unknown Source)
at jetbrains.mps.smodel.WorkbenchModelAccess$CommandRunnable.lambda$run$0(WorkbenchModelAccess.java:449)
at jetbrains.mps.smodel.WriteActionDispatcher.run(WriteActionDispatcher.java:39)
at jetbrains.mps.smodel.WorkbenchModelAccess.lambda$runWriteAction$1(WorkbenchModelAccess.java:105)
at com.intellij.openapi.application.impl.ApplicationImpl.runWriteAction(ApplicationImpl.java:1010)
at jetbrains.mps.smodel.WorkbenchModelAccess.runWriteAction(WorkbenchModelAccess.java:113)
at jetbrains.mps.smodel.WorkbenchModelAccess$CommandRunnable.run(WorkbenchModelAccess.java:446)
at com.intellij.openapi.command.impl.CoreCommandProcessor.executeCommand(CoreCommandProcessor.java:137)
at com.intellij.openapi.command.impl.CoreCommandProcessor.executeCommand(CoreCommandProcessor.java:95)
at com.intellij.openapi.command.impl.CoreCommandProcessor.executeCommand(CoreCommandProcessor.java:85)
at jetbrains.mps.smodel.WorkbenchModelAccess.runWriteActionInCommand(WorkbenchModelAccess.java:311)
at jetbrains.mps.smodel.WorkbenchModelAccess.executeCommand(WorkbenchModelAccess.java:307)
at jetbrains.mps.project.ProjectModelAccess.executeCommand(ProjectModelAccess.java:43)
at org.campagnelab.ui.code.Swing.Button$1.actionPerformed(Unknown Source)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6541)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3325)
at java.awt.Component.processEvent(Component.java:6306)
at java.awt.Container.processEvent(Container.java:2237)
at java.awt.Component.dispatchEventImpl(Component.java:4897)
at java.awt.Container.dispatchEventImpl(Container.java:2295)
at java.awt.Component.dispatchEvent(Component.java:4719)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4889)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4526)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4467)
at java.awt.Container.dispatchEventImpl(Container.java:2281)
at java.awt.Window.dispatchEventImpl(Window.java:2746)
at java.awt.Component.dispatchEvent(Component.java:4719)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:764)
at java.awt.EventQueue.access$500(EventQueue.java:98)
at java.awt.EventQueue$3.run(EventQueue.java:715)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90)
at java.awt.EventQueue$4.run(EventQueue.java:737)
at java.awt.EventQueue$4.run(EventQueue.java:735)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:734)
at com.intellij.ide.IdeEventQueue.defaultDispatchEvent(IdeEventQueue.java:779)
at com.intellij.ide.IdeEventQueue._dispatchEvent(IdeEventQueue.java:716)
at com.intellij.ide.IdeEventQueue.dispatchEvent(IdeEventQueue.java:395)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Workflow name must escape spaces

I created a workflow called 'Split by Species'. When I tried to run the workflow, the run config failed with:
BUILD FAILED
Target "by" does not exist in the project "nextflow-local".

As a workaround I will remove the spaces from the name of the workflow.
A fix is needed to escape the spaces with underscore in the workflow name.

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