Every now and then I get a failure in samplesheets with a tumor-only (with PoN) run with a samplesheet where the error says the opposite of what the samplesheet is (see below), I fix it and every time I forget what I did...

sample,fastq_1,fastq_2,patient,status
001_11_21311_SX1L,/home/incalci/shared/runs/Iolanthe/FFPE/raw-data/run_2026-01-13/.//251223_VH00607_396_AAGNHKWM5/001_11_21311_SX1L_S8_R1_001.fastq.gz,/home/incalci/shared/runs/Iolanthe/FFPE/raw-data/run_2026-01-13/.//251223_VH00607_396_AAGNHKWM5/001_11_21311_SX1L_S8_R2_001.fastq.gz,001_11_21311_SX1L,1                    
002_11_21311_1VO4,/home/incalci/shared/runs/Iolanthe/FFPE/raw-data/run_2026-01-13/.//251223_VH00607_396_AAGNHKWM5/002_11_21311_1VO4_S9_R1_001.fastq.gz,/home/incalci/shared/runs/Iolanthe/FFPE/raw-data/run_2026-01-13/.//251223_VH00607_396_AAGNHKWM5/002_11_21311_1VO4_S9_R2_001.fastq.gz,002_11_21311_1VO4,1                    
003_11_21311_13YJ,/home/incalci/shared/runs/Iolanthe/FFPE/raw-data/run_2026-01-13/.//251223_VH00607_396_AAGNHKWM5/003_11_21311_13YJ_S10_R1_001.fastq.gz,/home/incalci/shared/runs/Iolanthe/FFPE/raw-data/run_2026-01-13/.//251223_VH00607_396_AAGNHKWM5/003_11_21311_13YJ_S10_R2_001.fastq.gz,003_11_21311_13YJ,1

Note that

status

is 1. But what I see in the nextflow log is

2:02.737 [Actor Thread 18] ERROR nextflow.Nextflow - Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>
Jan-13 11:42:02.738 [Task monitor] DEBUG n.processor.TaskPollingMonitor - <<< barrier arrives (monitor: slurm) - terminating tasks monitor poll loop
Jan-13 11:42:02.739 [main] DEBUG nextflow.Session - Session await > all processes finished
Jan-13 11:42:02.739 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jan-13 11:42:02.739 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=3; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Jan-13 11:42:02.741 [Actor Thread 32] ERROR nextflow.extension.OperatorImpl - @unknown
nextflow.exception.WorkflowScriptErrorException: The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : mutect2

Which frankly makes no sense... EDIT: For some reason

lane

is required although the docs say it is optional. With

lane

set, the error goes away.

yes. See github issues sad cowboy, we got a number of them but despite spending a lot of time on hit have no idea why. Let me see if claude has any clue

In this specific case it works after adding a lane column (??)