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Use of input repeaters ("each") in DSL2
Not sure I'm missing something super obvious, but is each supported in DSL2? The following doesn't work:
nextflow.enable.dsl=2
numbers = Channel.of(1, 2, 3)
letters = Channel.of('A', 'B')
process test {
echo true
input:
each val(number)
val(letter)
script:
"""
echo $number $letter
"""
}
workflow {
test(numbers, letters)
}
I would have expected to see an output like (with possibly different order, etc):
1 A
2 A
3 A
1 B
2 B
3 B
Instead, I get:
N E X T F L O W ~ version 20.07.1
Launching `test.nf` [tiny_davinci] - revision: f20ada7690
No such variable: number
-- Check script 'test.nf' at line: 10 or see '.nextflow.log' file for more details
Here's the nextflow log:
Mar-11 22:24:41.226 [main] DEBUG nextflow.cli.Launcher - $> nextflow run test.nf
Mar-11 22:24:41.459 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 20.07.1
Mar-11 22:24:41.475 [main] INFO nextflow.cli.CmdRun - Launching `test.nf` [tiny_davinci] - revision: f20ada7690
Mar-11 22:24:41.497 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: ####
Mar-11 22:24:41.498 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: ####
Mar-11 22:24:41.526 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Mar-11 22:24:42.024 [main] DEBUG nextflow.Session - Session uuid: d9ea5922-42be-42e0-ac92-4e043667b0c2
Mar-11 22:24:42.024 [main] DEBUG nextflow.Session - Run name: tiny_davinci
Mar-11 22:24:42.025 [main] DEBUG nextflow.Session - Executor pool size: 8
Mar-11 22:24:42.230 [main] DEBUG nextflow.cli.CmdRun -
Version: 20.07.1 build 5412
Created: 24-07-2020 15:18 UTC
System: Linux 3.10.0-1127.19.1.el7.x86_64
Runtime: Groovy 2.5.11 on OpenJDK 64-Bit Server VM 11.0.2+9
Encoding: UTF-8 (UTF-8)
Process: ####
CPUs: 8 - Mem: 62 GB (12.3 GB) - Swap: 0 (0)
Mar-11 22:24:42.283 [main] DEBUG nextflow.Session - Work-dir: ####
Mar-11 22:24:42.351 [main] DEBUG nextflow.Session - Observer factory: TowerFactory
Mar-11 22:24:42.355 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Mar-11 22:24:42.716 [main] DEBUG nextflow.Session - Session start invoked
Mar-11 22:24:42.924 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Mar-11 22:24:43.010 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: test
Mar-11 22:24:43.074 [main] DEBUG nextflow.Session - Session aborted -- Cause: Unknown variable 'number'
Mar-11 22:24:43.087 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: Unknown variable 'number'
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:74)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:237)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:265)
at nextflow.script.ProcessConfig.getProperty(ProcessConfig.groovy:273)
at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190)
at groovy.lang.Closure.getPropertyTryThese(Closure.java:313)
at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:303)
at groovy.lang.Closure.getProperty(Closure.java:288)
at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:49)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:309)
at Script_6d4d1d16$_runScript_closure1.doCall(Script_6d4d1d16:10)
at Script_6d4d1d16$_runScript_closure1.doCall(Script_6d4d1d16)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
at groovy.lang.Closure.call(Closure.java:405)
at groovy.lang.Closure.call(Closure.java:399)
at nextflow.script.ProcessDef.initialize(ProcessDef.groovy:111)
at nextflow.script.ProcessDef.run(ProcessDef.groovy:165)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
at nextflow.script.ComponentDef.invoke_o(ComponentDef.groovy:41)
at nextflow.script.WorkflowBinding.invokeMethod(WorkflowBinding.groovy:90)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeOnDelegationObjects(ClosureMetaClass.java:397)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:339)
at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.callCurrent(PogoMetaClassSite.java:64)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
at Script_6d4d1d16$_runScript_closure2$_closure4.doCall(Script_6d4d1d16:20)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
at groovy.lang.Closure.call(Closure.java:405)
at groovy.lang.Closure.call(Closure.java:399)
at nextflow.script.WorkflowDef.run0(WorkflowDef.groovy:182)
at nextflow.script.WorkflowDef.run(WorkflowDef.groovy:169)
at nextflow.script.BindableDef.invoke_a(BindableDef.groovy:52)
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:115)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:127)
at nextflow.script.BaseScript.runDsl2(BaseScript.groovy:191)
at nextflow.script.BaseScript.run(BaseScript.groovy:200)
at nextflow.script.ScriptParser.runScript(ScriptParser.groovy:219)
at nextflow.script.ScriptRunner.run(ScriptRunner.groovy:219)
at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:127)
at nextflow.cli.CmdRun.run(CmdRun.groovy:274)
at nextflow.cli.Launcher.run(Launcher.groovy:466)
at nextflow.cli.Launcher.main(Launcher.groovy:648)
Great, thanks for that tip! As you say, it works if you leave off the val qualifier.
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