A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

sarekrun.txt

execution_trace_2026-02-23_10-25-55.txt

16Feb2026_batch1_2_a.csv

I think I'm encountering something similar to <https://nfcore.slack.com/archives/CGFUX04HZ/p1771861585217959|Vimel above>, with missing outputs and no errors. Here is the execution trace, run command and sample sheet.
Note: my setup includes tumours sequenced across two lanes, but indicated as such in the samplesheet, and have UMIs encoded in the R1's with the structure specified in the run command.

I really can't see what I'm doing wrong, but I don't have variant calls for these tumour samples.

Oh, I think it might be this: <https://github.com/nf-core/sarek/issues/2118>

Which looks like it'll be fixed in the next release?

I ran it with `-r fix/syntax-preprocessing` and it doesn't seem to help.

You could test older sarek versions with `-r` to see if there was a regression ...