Develop Branch: Unable to Store Cases

[ivadym]

Describe the bug

It's not possible to store any cases in Housekeeper. This issue affects all workflows.

To Reproduce

• /home/proj/stage/bin/miniconda3/envs/S_hermes/bin/hermes convert deliverables ...
• cg workflow <workflow> store <case>

Expected behavior

• Cases should be successfully stored in Housekeeper.

If workflow, which rules

• balsamic-qc

  balsamic hasta.scilifelab.se 2023-10-17 10:33:14 snakemake.logging pid:226536 [ERROR] AttributeError in file /home/proj/stage/bin/miniconda3/envs/S_balsamic/lib/python3.11/site-packages/BALSAMIC/workflows/QC.smk, line 136: 'list' object has no attribute 'keys'

• balsamic (WGS, TGA) and balsamic-umi

2023-10-17 10:37:37 hasta.scilifelab.se cg_hermes.deliverables[233561] INFO Parsing deliverables for balsamic 2023-10-17 10:37:37 hasta.scilifelab.se cg_hermes.deliverables[233561] WARNING Mandatory file (tumor-cram, cram) is missing 2023-10-17 10:37:37 hasta.scilifelab.se cg_hermes.deliverables[233561] WARNING Mandatory file (tumor-cram-index, cram) is missing 2023-10-17 10:37:37 hasta.scilifelab.se cg_hermes.cli.convert[233561] ERROR Deliverables is missing mandatory files

Proposed solution

• [x] balsamic-qc: adapt QC.smk to the new sample structure (list, not dict) (https://github.com/Clinical-Genomics/BALSAMIC/pull/1295)
• [x] balsamic: include cram files in the HK deliverable file (https://github.com/Clinical-Genomics/BALSAMIC/pull/1307)

Version (please complete the following information): balsamic --version develop

[pbiology]

Do we need to include this as a patch to 12?

[ivadym]

No, this is a bug in the develop branch. We have to solve it before releasing v13

[ivadym]

Addressed!