Missing annotated STR call VCF - in HK?

Clinical-Genomics / raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇

https://github.com/nf-core/raredisease

MIT License

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Missing annotated STR call VCF - in HK? #24

Open dnil opened 1 week ago

dnil commented 1 week ago

Description of the bug

Not entirely sure this is a pipeline issue - CASEID_repeat_expansion_stranger.vcf.gz exists after a run, and in the deliverables file. But then again, there are tags for it in both Hermes and CG. A typo somewhere, or a permissions issue somehow? The index is copied... 🙄 Seen for 3/3 cases investigated.

Command used and terminal output

No response

Relevant files

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System information

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jemten commented 1 week ago

Thanks for submitting @dnil we'll look into it.

ramprasadn commented 4 days ago

@peterpru have you noticed this issue in your tests?

dnil commented 4 days ago

You can see this with e.g. amusingmarmoset: the file is present in /home/proj/stage/analysis/cases/amusingmarmoset/repeat_expansions/ but not in e.g. /home/proj/stage/housekeeper-bundles/amusingmarmoset/2024-06-25/.

peterpru commented 4 days ago

@peterpru have you noticed this issue in your tests?

I can check it out, might have been missed in the PR.

dnil commented 4 days ago

Super! That analysis dir does bear the signs of quite a few reruns, so possibly it would still work if we get a full run from start to finish, but better safe...