ERROR ~ No such variable: ch_library #61

zhouzhendiao · 2023-07-29T14:24:27Z

Description of the bug

command:

nextflow run /path-to/nf-core-crisprseq-2.0.0/workflow \
    -preview \
    --analysis screening \
    --genome GRCh37 \
    -profile singularity \
    --igenomes_base /path-to/references \
    -offline \
    --outdir . \
    --input samplesheet.csv \
    -resume \
    --max_cpus 16 \
    --max_memory 64.GB \
    --max_time 256.h

samplesheet.csv

sample,fastq_1,fastq_2,condition
KO14,KO14_S1_L003_R1_001.fastq.gz,KO14_S1_L003_R2_001.fastq.gz,treatment
KO-control,KO_control_S6_L005_R1_001.fastq.gz,KO-control_S6_L005_R2_001.fastq.gz,control

output:

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/crisprseq for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7598497

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/crisprseq/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:INPUT_CHECK_... -
ERROR ~ No such variable: ch_library

 -- Check script '/path-to/nf-core-crisprseq-2.0.0/workflow/./workflows/crisprseq_screening.nf' at line: 108 or see '.nextflow.log' file for more details

crisprseq_screening.nf at line: 108

105         //
106         // MODULE: Run mageck count
107         //
108         MAGECK_COUNT (
109             joined,
110             ch_library
111         )
112
113         ch_versions = ch_versions.mix(MAGECK_COUNT.out.versions.first())
114
115
116         MAGECK_COUNT.out.count.map {
117         it -> it[1]
118         }.set { ch_counts }
119
120     } else {
121         Channel.fromPath(params.count_table)
122         .set { ch_counts }
123     }

.nextflow.log

Jul-29 22:10:07.018 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_single` matches labels `process_single` for process with name NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:INPUT_CHECK_SCREENING:SAMPLESHEET_CHECK_SCREENING
Jul-29 22:10:07.027 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-29 22:10:07.027 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-29 22:10:07.034 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
Jul-29 22:10:07.040 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=56; memory=251.6 GB; capacity=56; pollInterval=100ms; dumpInterval=5m
Jul-29 22:10:07.212 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withLabel:process_medium` matches labels `process_medium` for process with name NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:FASTQC
Jul-29 22:10:07.213 [main] DEBUG nextflow.script.ProcessConfig - Config settings `withName:FASTQC` matches process NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:FASTQC
Jul-29 22:10:07.216 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
Jul-29 22:10:07.217 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
Jul-29 22:10:07.247 [main] DEBUG nextflow.Session - Session aborted -- Cause: No such property: ch_library for class: nextflow.script.WorkflowBinding
Jul-29 22:10:07.266 [main] DEBUG nextflow.Session - The following nodes are still active:
  [operator] splitCsv
  [operator] map
  [operator] mix
  [operator] mix
  [operator] map
  [operator] reduce
  [operator] map

Jul-29 22:10:07.274 [main] ERROR nextflow.cli.Launcher - @unknown
groovy.lang.MissingPropertyException: No such property: ch_library for class: nextflow.script.WorkflowBinding
        at groovy.lang.Binding.getVariable(Binding.java:61)
        at nextflow.script.WorkflowBinding.getVariable(WorkflowBinding.groovy:140)
        at groovy.lang.Binding.getProperty(Binding.java:116)
        at nextflow.script.WorkflowBinding.getProperty(WorkflowBinding.groovy:129)
        at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190)
        at groovy.lang.Closure.getPropertyTryThese(Closure.java:320)
        at groovy.lang.Closure.getPropertyDelegateFirst(Closure.java:310)
        at groovy.lang.Closure.getProperty(Closure.java:296)
        at org.codehaus.groovy.runtime.callsite.PogoGetPropertySite.getProperty(PogoGetPropertySite.java:49)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:341)
        at Script_21dbb60c$_runScript_closure2$_closure4.doCall(Script_21dbb60c:108)
        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: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_54323686$_runScript_closure1$_closure3.doCall(Script_54323686:46)
        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: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_54323686$_runScript_closure2$_closure4.doCall(Script_54323686:61)
        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: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.IterableDef$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)

Command used and terminal output

No response

Relevant files

No response

System information

No response

The text was updated successfully, but these errors were encountered:

zhouzhendiao · 2023-07-30T03:42:14Z

OK， the issue above is because of lacking --library library.csv. But tutorial in screening part seems have no description about library.csv. One can find in MAGeCK document.

LaurenceKuhl · 2023-07-31T08:02:50Z

Hi @zhouzhendiao thanks a lot for reporting! :)
So just to be clear you got it running but what was lacking was the correct documentation? I'll add it.

zhouzhendiao · 2023-07-31T08:12:35Z

Hi @zhouzhendiao thanks a lot for reporting! :) So just to be clear you got it running but what was lacking was the correct documentation? I'll add it.

Thanks for replying!

I'm using screning sub-pipeline, the paramters --library library.csv in the command but lacking of detailed description :

nextflow run nf-core/crisprseq --analysis screening --input samplesheet.csv --library library.csv --outdir <OUTDIR> -profile docker

Maybe the format of library.csv is described in MAGeCK. Sorry that I'm not familiar with it. Can you kindly add this?

LaurenceKuhl · 2024-08-20T14:12:38Z

Hi we added examples in the documentation, let me know if it's still not clear enough you can re open this :) thanks a lot!

zhouzhendiao added the bug Something isn't working label Jul 29, 2023

LaurenceKuhl closed this as completed Aug 20, 2024

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ERROR ~ No such variable: ch_library #61

ERROR ~ No such variable: ch_library #61

zhouzhendiao commented Jul 29, 2023 •

edited

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zhouzhendiao commented Jul 30, 2023

LaurenceKuhl commented Jul 31, 2023

zhouzhendiao commented Jul 31, 2023

LaurenceKuhl commented Aug 20, 2024

ERROR ~ No such variable: ch_library #61

ERROR ~ No such variable: ch_library #61

Comments

zhouzhendiao commented Jul 29, 2023 • edited Loading

Description of the bug

Command used and terminal output

Relevant files

System information

zhouzhendiao commented Jul 30, 2023

LaurenceKuhl commented Jul 31, 2023

zhouzhendiao commented Jul 31, 2023

LaurenceKuhl commented Aug 20, 2024

zhouzhendiao commented Jul 29, 2023 •

edited

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