Missing annotated STR call VCF - in HK?

[dnil]

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

No response

System information

No response

[jemten]

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

[ramprasadn]

@peterpru have you noticed this issue in your tests?

[dnil]

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]

@peterpru have you noticed this issue in your tests?

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

[dnil]

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...