Commit 4a63eb68 authored by jkvis's avatar jkvis

Update notes_2017_06_06.md

parent a5ef673f
# Work discussion 23-05-2017
Present: Jonathan Vis (JV), Gerben van der Vries (GV), Jeroen Laros (JL),
Rowan Kanninga (RK), Leon Mei (LM), Mark Santcroos (MS).
## GoNL re-analysis
- There is a discordance between the variant calls from the pipeline runs in
Groningen and Leiden.
- Calls for the Genome in a bottle samples (GITB) are identical.
- LM asks for a log of the commands for both pipelines.
- QC of truth set of the GITB samples still needs to be done.
- LM ask for a method to collect QC metrics.
- Storage: We need at least 10T of HPC storage, 10T of LT storage.
- PN: We need to check concordance, array and liftover before we deliver.
## eLAN
Resolved.
## CoManage
- 24-05-2017 Mark will have the hands-on session.
- PN: Has worked on authorisation workflow. Potential issues with multiple
group memberships and deleting on of these groups. Do we do this locally or
globally? Meeting at SURF, 24-05-2017.
- LM: Do we need other people (DICT, Leiden).
- No test-IDP at the UMCG or LUMC. AP: JL will contact DICT.
## Ansible and Easybuild integration
- PN made an idempotent playbook, checking handlers now.
## Closing remarks
- LM has contact with the Imaging WP about Ansible.
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# Work discussion 06-06-2017
Present: Jonathan Vis (JV), Jeroen Laros (JL),
Rowan Kanninga (RK), Leon Mei (LM), Mark Santcroos (MS).
## GoNL re-analysis
- Issues with pipeline settings, have been resolved now.
- Documenting the actual versions of the tools that are used; the
headers/footers (backend specific code) are obscuring the logic.
- Testing on chr Y (genome in a bottle).
- Re-run GIAB sample (started).
- No X11 on shark for QC output (LM looks it to this).
## eLAN
Resolved.
## CoManage
- MS: waiting on Surf for the implementation of a secure transport mechanism.
- PN: what about robustness; no concerns at the moment.
- MS: Leiden does not have a test IDP.
- MS: will ask Surf about progress.
- JL: do we need a test IDP? PN: likes to see the integration with surf connext;
MS: IDP will not be the main issue, the workflow is the main issue.
- PN likes to have a roadmap from Surf; (JL and) PN will draft an e-mail.
## Ansible and Easybuild integration
- PN made an idempotent playbook, checking handlers now; progress is slow.
- PN playbook is ok, but could be improved upon.
- Playbook is on GitHub: https://github.com/bbmri-nl/bbmri-nl-pipeline-deployment.
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