Did you ever see this error:

Test [b16676c2] '-profile test --tools merge,snpeff,vep' FAILED (56.733s)

  Assertion failed: 
  
  assert workflow.success
         |        |
         workflow false
  
  Nextflow stdout:
  
  ERROR ~ Invalid method invocation `call` with arguments: [[patient:test, sample:test, sex:NA, status:0, id:test, data_type:vcf, variantcaller:, file_name:test.vcf], NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF, snpeff, /mnt/lustre/groups/nahnsen/nahbu450/nf-core/sarek/.nf-test/tests/b16676c214a0b7af8158f6aab0d5772d/work/e6/4ff1f6ef95f1e7f47f60d7fc622a19/test_snpEff.csv] (java.util.ArrayList) on _closure4 type

from the message it seems like the process name instead of the file is passed???

I have seen this before

And the concatenate tests I cant get to run because mutect always complains

working on getting the tests to pass on this PR: https://github.com/nf-core/sarek/pull/2138 but its so tedious and I need to do other stuff at some point

the number of changes is huge. can we break this PR down to help find the cause

its just updating two nf-core subworkflows and the bcftools suite

🤷‍♀️ maybe we can just start with the bcftools one that affects snpeff and keep the rest for a separate PR. something is going wrong somewhere

I will divide it

sometimes i am really doubting the one tool per process approach and one of the major reasons I don't love putting subworkflows into nf-core/modules

I always think yes this is the last big migration

absolutely and the fact that running all tests takes hours. I am wondering if we should have a separate action that runs all stub tests and only if those succeed then run the full blown thing

same error now occurs on the new PR

and it works locally, yes?

checking again now

at least it's reproducible

asking because the merge test did definitely work yesterday: https://github.com/nf-core/sarek/actions/runs/21913480935/job/63293132723?pr=2137 Ok my best guess is something on the snpeff output. I am sort of guessing something around the parsing of multiqc_files or the writing of the csv files. Let me run this locally to get more logs

yay

yep we just talked about it