Open
Description
openedon Oct 3, 2024
Description of the bug
When running the nf-core/sarek pipeline with a sample sheet in which samples are not unique, the pipeline runs and fails only after the alignment step (I believe, at GATK4_MARKDUPLICATES process).
When carefully checking the documentation at nf-core/sarek, I realised that samples should be unique:
Custom sample ID for each tumor and normal sample; more than one tumor sample for each subject is possible, i.e. a tumor and a relapse; samples can have multiple lanes for which the same ID must be used to merge them later (see also lane). Sample IDs must be unique for unique biological samples
Would be useful to add a check to stop the pipeline in case non-unique sample IDs are provided.
Samplesheet used:
patient,status,sample,lane,fastq_1,fastq_2
F2407718,0,monolayer,L1,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407718_R1_combined.fastq.gz,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407718_R2_combined.fastq.gz
F2407719,0,monolayer,L1,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407719_R1_combined.fastq.gz,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407719_R2_combined.fastq.gz
F2407720,0,monolayer,L1,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407720_R1_combined.fastq.gz,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407720_R2_combined.fastq.gz
F2407721,1,monolayer,L1,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407721_R1_combined.fastq.gz,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407721_R2_combined.fastq.gz
F2407722,1,monolayer,L1,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407722_R1_combined.fastq.gz,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407722_R2_combined.fastq.gz
F2407723,1,monolayer,L1,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407723_R1_combined.fastq.gz,/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/F2407723_R2_combined.fastq.gz
Parameters file used:
{
"input": "/mnt/titan/mcasanova/ctDNA/01_samples/CHUgeneve/CHUgeneve_samplelist.csv",
"wes": true,
"tools": "mutect2,vep,snpeff",
"aligner": "bwa-mem2",
"vep_custom_args": "everything",
"save_mapped": true,
"save_output_as_bam": true,
"genome": "GATK.GRCh38",
"save_reference": true
}
Command used and terminal output
$ nextflow run nf-core/sarek -profile docker --outdir ./results -resume -params-file nf-param.json -with-report -with-trace -with-dag flowchart.png -with-timeline timeline.html
nextflow.exception.AbortOperationException: Detected join operation duplicate emission on left channel -- offending element: key=[patient:F2407719, sample:monolayer, sex:NA, status:0, n_fastq:12, data_type:bam, id:monolayer]; value=/mnt/titan/mcasanova/ctDNA/03_analysis_CHU/work/7f/5a1152a34ee73b2a2262a119788472/monolayer.sorted.bam
at nextflow.extension.JoinOp.checkForDuplicate(JoinOp.groovy:266)
at nextflow.extension.JoinOp.join0(JoinOp.groovy:177)
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:569)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at groovy.lang.MetaClassImpl.doInvokeMethod(MetaClassImpl.java:1333)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1088)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:645)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:628)
at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:82)
at nextflow.extension.JoinOp$_handler_closure1.doCall(JoinOp.groovy:117)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.extension.DataflowHelper$_subscribeImpl_closure2.doCall(DataflowHelper.groovy:287)
at jdk.internal.reflect.GeneratedMethodAccessor134.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:569)
at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:343)
at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:328)
at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:279)
at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1007)
at groovy.lang.Closure.call(Closure.java:433)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120)
at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108)
at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43)
at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293)
at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30)
at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93)
at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
at java.base/java.lang.Thread.run(Thread.java:840)
Relevant files
No response
System information
- Nextflow version 24.04.4
- Workstation
- Local
- Docker
- Ubuntu Linux
- nf-core/sarek v3.4.4-g5cc3049
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