Function for mapcombinemultimap #339

jfy133 · 2023-07-27T13:01:22Z

Extremely naïve attempt to create a map -> combine -> multiMap function (second suggestion to close #207 ), however this currently fails due to a

Missing process or function doCall()

<...>

Caused by: groovy.lang.MissingMethodException: No signature of method: WorkflowTaxprofiler$_mapCombineMultimap_closure2.doCall() is applicable for argument types: () values: []
Possible solutions: doCall(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object), isCase(java.lang.Object), isCase(java.lang.Object), findAll(), findAll(), f
indAll(groovy.lang.Closure)

error... I'm not sure what is causing this

Test command:

nextflow run ../main.nf -profile singularity,test_nothing --run_centrifuge --outdir ./results -dump-channels

I tried to base the structure of the code on: https://github.com/Midnighter/nextflow-utility-services/blob/main/lib/CustomChannelOperators.groovy

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/taxprofiler branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

github-actions · 2023-07-27T13:03:54Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit e38b36a

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

files_exist - File found: .gitattributes
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files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
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files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-taxprofiler_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-taxprofiler_logo_light.png
files_exist - File found: docs/images/nf-core-taxprofiler_logo_dark.png
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files_exist - File found: docs/README.md
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files_exist - File found: lib/WorkflowMain.groovy
files_exist - File found: main.nf
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files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: lib/WorkflowTaxprofiler.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
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files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: bin/markdown_to_html.r
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files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
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files_exist - File not found check: .markdownlint.yml
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files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 1.1.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
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files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - lib/nfcore_external_java_deps.jar matches the template
files_unchanged - lib/NfcoreTemplate.groovy matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
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actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
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actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (191 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.9
Run at 2023-08-01 07:51:17

lib/WorkflowTaxprofiler.groovy

jfy133 · 2023-07-28T20:07:01Z

With your suggestion:

    static mapCombineMultimap(ch_profile, ch_database) {

        ch_prepped_channel = ch_profile
            .map { meta, profile -> [meta.db_name, meta, profile] }
            .combine(ch_database, by: 0)
            .multiMap {
                key, meta, profile, db_meta, db ->
                    profile: [meta, profile]
                    db: db
            }

        return ch_prepped_channel
    }

I get the following:

$ nextflow run ../main.nf -profile singularity,test_nothing --run_centrifuge --outdir ./results -dump-channels
N E X T F L O W  ~  version 23.04.1
Launching `../main.nf` [zen_descartes] DSL2 - revision: e2bcf7b1a1
ERROR ~ BUG! exception in phase 'semantic analysis' in source unit 'Script_25d1d7c6' The lookup for WorkflowTaxprofiler caused a failed compilation. There should not have been any compilation from this call.

 -- Check script '/home/james/git/nf-core/taxprofiler/main.nf' at line: 52 or see '.nextflow.log' file for more details

in teh log

Jul-28 22:05:10.469 [main] DEBUG nextflow.Session - Session aborted -- Cause: BUG! exception in phase 'semantic analysis' in source unit 'Script_25d1d7c6' The lookup for WorkflowTaxprofiler caused a failed compilation. There should not have been any compilation from this call.
Jul-28 22:05:10.487 [main] ERROR nextflow.cli.Launcher - @unknown
org.codehaus.groovy.GroovyBugError: BUG! exception in phase 'semantic analysis' in source unit 'Script_25d1d7c6' The lookup for WorkflowTaxprofiler caused a failed compilation. There should not have been any compilation from this call.
        at org.codehaus.groovy.control.ClassNodeResolver.findByClassLoading(ClassNodeResolver.java:214)
        at org.codehaus.groovy.control.ClassNodeResolver.tryAsLoaderClassOrScript(ClassNodeResolver.java:198)
        at org.codehaus.groovy.control.ClassNodeResolver.findClassNode(ClassNodeResolver.java:169)
        at org.codehaus.groovy.control.ClassNodeResolver.resolveName(ClassNodeResolver.java:125)
        at org.codehaus.groovy.control.ResolveVisitor.resolveToOuter(ResolveVisitor.java:869)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:506)
        at org.codehaus.groovy.control.ResolveVisitor.resolve(ResolveVisitor.java:468)
        at org.codehaus.groovy.control.ResolveVisitor.transformVariableExpression(ResolveVisitor.java:1129)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:888)
        at org.codehaus.groovy.control.ResolveVisitor.transformMethodCallExpression(ResolveVisitor.java:1274)
        at org.codehaus.groovy.control.ResolveVisitor.transform(ResolveVisitor.java:896)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitExpressionStatement(ClassCodeExpressionTransformer.java:108)
        at org.codehaus.groovy.ast.stmt.ExpressionStatement.visit(ExpressionStatement.java:40)
        at org.codehaus.groovy.ast.CodeVisitorSupport.visitBlockStatement(CodeVisitorSupport.java:86)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitBlockStatement(ClassCodeVisitorSupport.java:164)
        at org.codehaus.groovy.control.ResolveVisitor.visitBlockStatement(ResolveVisitor.java:1566)
        at org.codehaus.groovy.ast.stmt.BlockStatement.visit(BlockStatement.java:69)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClassCodeContainer(ClassCodeVisitorSupport.java:138)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitConstructorOrMethod(ClassCodeVisitorSupport.java:111)
        at org.codehaus.groovy.ast.ClassCodeExpressionTransformer.visitConstructorOrMethod(ClassCodeExpressionTransformer.java:66)
        at org.codehaus.groovy.control.ResolveVisitor.visitConstructorOrMethod(ResolveVisitor.java:294)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitMethod(ClassCodeVisitorSupport.java:106)
        at org.codehaus.groovy.ast.ClassNode.visitMethods(ClassNode.java:1094)
        at org.codehaus.groovy.ast.ClassNode.visitContents(ClassNode.java:1087)
        at org.codehaus.groovy.ast.ClassCodeVisitorSupport.visitClass(ClassCodeVisitorSupport.java:52)
        at org.codehaus.groovy.control.ResolveVisitor.visitClass(ResolveVisitor.java:1483)
        at org.codehaus.groovy.control.ResolveVisitor.startResolving(ResolveVisitor.java:262)
        at org.codehaus.groovy.control.CompilationUnit.lambda$new$16(CompilationUnit.java:739)
        at org.codehaus.groovy.control.CompilationUnit$ISourceUnitOperation.doPhaseOperation(CompilationUnit.java:902)
        at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:628)
        at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:389)
        at groovy.lang.GroovyClassLoader.lambda$parseClass$3(GroovyClassLoader.java:332)
        at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
        at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:330)
        at groovy.lang.GroovyShell.parseClass(GroovyShell.java:526)
        at groovy.lang.GroovyShell.parse(GroovyShell.java:538)
        at groovy.lang.GroovyShell.parse(GroovyShell.java:570)
        at nextflow.script.ScriptParser.parse(ScriptParser.groovy:169)
        at nextflow.script.ScriptParser.parse(ScriptParser.groovy:194)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:214)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:205)
        at nextflow.script.IncludeDef.memoizedMethodPriv$loadModule0PathMapSession(IncludeDef.groovy:151)
        at nextflow.script.IncludeDef.access$0(IncludeDef.groovy)
        at nextflow.script.IncludeDef$__clinit__closure2.doCall(IncludeDef.groovy)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
        at nextflow.script.IncludeDef.loadModule0(IncludeDef.groovy)
        at nextflow.script.IncludeDef.load0(IncludeDef.groovy:123)
        at nextflow.script.IncludeDef$load0$1.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at Script_1a59717b.runScript(Script_1a59717b:52)
        at nextflow.script.BaseScript.run0(BaseScript.groovy:145)
        at nextflow.script.BaseScript.run(BaseScript.groovy:192)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:229)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:224)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:130)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
        at nextflow.cli.Launcher.run(Launcher.groovy:494)
        at nextflow.cli.Launcher.main(Launcher.groovy:653)
Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed:
/home/james/git/nf-core/taxprofiler/lib/WorkflowTaxprofiler.groovy: 261: Apparent variable 'ch_prepped_channel' was found in a static scope but doesn't refer to a local variable, static field or class. Possible causes:
You attempted to reference a variable in the binding or an instance variable from a static context.
You misspelled a classname or statically imported field. Please check the spelling.
You attempted to use a method 'ch_prepped_channel' but left out brackets in a place not allowed by the grammar.
 @ line 261, column 9.
           ch_prepped_channel = ch_profile
           ^

/home/james/git/nf-core/taxprofiler/lib/WorkflowTaxprofiler.groovy: 270: Apparent variable 'ch_prepped_channel' was found in a static scope but doesn't refer to a local variable, static field or class. Possible causes:
You attempted to reference a variable in the binding or an instance variable from a static context.
You misspelled a classname or statically imported field. Please check the spelling.
You attempted to use a method 'ch_prepped_channel' but left out brackets in a place not allowed by the grammar.
 @ line 270, column 16.
           return ch_prepped_channel
                  ^

2 errors

        at org.codehaus.groovy.control.ErrorCollector.failIfErrors(ErrorCollector.java:292)
        at org.codehaus.groovy.control.CompilationUnit$IPrimaryClassNodeOperation.doPhaseOperation(CompilationUnit.java:985)
        at org.codehaus.groovy.control.CompilationUnit.processPhaseOperations(CompilationUnit.java:672)
        at org.codehaus.groovy.control.CompilationUnit.compile(CompilationUnit.java:636)
        at groovy.lang.GroovyClassLoader.doParseClass(GroovyClassLoader.java:389)
        at groovy.lang.GroovyClassLoader.lambda$parseClass$3(GroovyClassLoader.java:332)
        at org.codehaus.groovy.runtime.memoize.StampedCommonCache.compute(StampedCommonCache.java:163)
        at org.codehaus.groovy.runtime.memoize.StampedCommonCache.getAndPut(StampedCommonCache.java:154)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:330)
        at groovy.lang.GroovyClassLoader.parseClass(GroovyClassLoader.java:314)
        at groovy.lang.GroovyClassLoader.recompile(GroovyClassLoader.java:954)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:910)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:979)
        at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:574)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:869)
        at groovy.lang.GroovyClassLoader.loadClass(GroovyClassLoader.java:745)
        at org.codehaus.groovy.control.ClassNodeResolver.findByClassLoading(ClassNodeResolver.java:209)
        ... 72 common frames omitted

jfy133 · 2023-07-28T20:09:40Z

Prepending def to ch_prepped_channel = doesn't work (as I sort of expect as it's not a variable.) with a 'Missing process or function doCall()' error,

And instead prepending back DataflowBroadcast does the same (e.g DataflowBroadcast ch_prepped_channel = ch_profile gives a Missing process or function doCall() console log error, and .nextflow.log error below)

Jul-28 22:08:23.087 [main] ERROR nextflow.cli.Launcher - @unknown
nextflow.exception.MissingProcessException: Missing process or function doCall()
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:191)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
        at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
        at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
        at Script_25d1d7c6$_runScript_closure2$_closure4.doCall(Script_25d1d7c6:248)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
        at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
        at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
        at Script_1a59717b$_runScript_closure1$_closure3.doCall(Script_1a59717b:58)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
        at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:40)
        at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:102)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:408)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:350)
        at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:61)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
        at Script_1a59717b$_runScript_closure2$_closure4.doCall(Script_1a59717b:72)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
        at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:51)
        at nextflow.script.ChainableDef$invoke_a.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at nextflow.script.BaseScript.run0(BaseScript.groovy:183)
        at nextflow.script.BaseScript.run(BaseScript.groovy:192)
        at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:229)
        at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:224)
        at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:130)
        at nextflow.cli.CmdRun.run(CmdRun.groovy:368)
        at nextflow.cli.Launcher.run(Launcher.groovy:494)
        at nextflow.cli.Launcher.main(Launcher.groovy:653)
Caused by: groovy.lang.MissingMethodException: No signature of method: WorkflowTaxprofiler$_mapCombineMultimap_closure2.doCall() is applicable for argument types: () values: []
Possible solutions: doCall(java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object, java.lang.Object), isCase(java.lang.Object), isCase(java.lang.Object), findAll(), findAll(), findAll(groovy.lang.Closure)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:266)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.extension.MultiMapOp.<init>(MultiMapOp.groovy:41)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
        at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480)
        at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:72)
        at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
        at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:110)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:286)
        at nextflow.extension.OperatorImpl.multiMap(OperatorImpl.groovy:1227)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1258)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:147)
        at nextflow.extension.OpCall.invoke1(OpCall.groovy:317)
        at nextflow.extension.OpCall.invoke0(OpCall.groovy:303)
        at nextflow.extension.OpCall.invoke(OpCall.groovy:163)
        at nextflow.extension.OpCall.call(OpCall.groovy:113)
        at nextflow.plugin.extension.PluginExtensionProvider.invokeExtensionMethod(PluginExtensionProvider.groovy:282)
        at groovy.runtime.metaclass.NextflowDelegatingMetaClass.invokeMethod(NextflowDelegatingMetaClass.java:58)
        at org.codehaus.groovy.runtime.callsite.PojoMetaClassSite.call(PojoMetaClassSite.java:44)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139)
        at WorkflowTaxprofiler.mapCombineMultimap(WorkflowTaxprofiler.groovy:262)
        at WorkflowTaxprofiler$mapCombineMultimap$0.call(Unknown Source)
        at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:125)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:148)
        at Script_05b7b79d$_runScript_closure1$_closure2.doCall(Script_05b7b79d:242)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:568)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035)
        at groovy.lang.Closure.call(Closure.java:412)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:204)
        at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:188)
        ... 79 common frames omitted

The placement of the function is debatable, but to have its definition evaluated by nextflow, rather than pure Groovy makes it work.

Midnighter · 2023-07-30T08:36:52Z

I couldn't fully test this as I was working in a codespace, but the original error went away by moving the function to a nextflow module. Let's see what the test suite says.

jfy133 · 2023-08-02T07:20:12Z

include still didn't work :( for now I'm happy with what we have (even if still slightly suboptiomal, if it's OK with you @Midnighter ?

jfy133 added 3 commits July 27, 2023 13:54

Get function to 'compile' at least...

7d588c0

Document function

a68f1ee

Remove debugging

baf3536

jfy133 requested a review from Midnighter July 27, 2023 13:01

jfy133 marked this pull request as draft July 27, 2023 13:01

Midnighter reviewed Jul 27, 2023

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lib/WorkflowTaxprofiler.groovy Outdated Show resolved Hide resolved

Midnighter added 2 commits July 30, 2023 08:34

refactor: move function to nextflow module, rename

6c93c10

The placement of the function is debatable, but to have its definition evaluated by nextflow, rather than pure Groovy makes it work.

chore: clean up module

8d47f72

Midnighter and others added 2 commits July 30, 2023 10:53

Merge branch 'dev' into function-for-mapcombinemultimap

3be05ce

Use function everywhwere

e38b36a

jfy133 marked this pull request as ready for review August 1, 2023 07:51

jfy133 requested review from Midnighter and a team August 1, 2023 07:51

Midnighter approved these changes Aug 2, 2023

View reviewed changes

jfy133 merged commit 7963917 into dev Aug 2, 2023
20 checks passed

jfy133 deleted the function-for-mapcombinemultimap branch August 2, 2023 07:25

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Function for mapcombinemultimap #339

Function for mapcombinemultimap #339

jfy133 commented Jul 27, 2023 •

edited

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jfy133 commented Jul 28, 2023

jfy133 commented Jul 28, 2023

Midnighter commented Jul 30, 2023

jfy133 commented Aug 2, 2023

Function for mapcombinemultimap #339

Function for mapcombinemultimap #339

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jfy133 commented Jul 27, 2023 • edited Loading

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

✅ Tests passed:

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jfy133 commented Jul 28, 2023

jfy133 commented Jul 28, 2023

Midnighter commented Jul 30, 2023

jfy133 commented Aug 2, 2023

jfy133 commented Jul 27, 2023 •

edited

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`nf-core lint` overall result: Passed ✅ ⚠️