Commit 4684ee0d authored by Laros's avatar Laros

Update notes_2017_05_09.md

parent b58a3ea4
# Work discussion 25-04-2017
# Work discussion 23-05-2017
Present: Jonathan Vis (JV), Pieter Neerincx (PN), Gerben van der Vries (GV),
Peter van 't Hof (PH), Jeroen Laros (JL), Rowan Kanninga (RK), Leon Mei (LM).
Present: Jonathan Vis (JV), Gerben van der Vries (GV), Jeroen Laros (JL),
Rowan Kanninga (RK), Leon Mei (LM), Mark Santcroos (MS).
## GoNL re-analysis
- GV: Started testing with the Molgenis framework, Experienced some memory
issues. They seem to be solved now.
- Some tools in the pipeline were updated (R + R scripts), input for cutadapt
(reverse complement) was fixed.
- Check cutadapt sequences, BWA and R version, AP: LM.
- Picard module 2.9.0 on UMCG cluster is pointing to the wrong version. AP: PN.
- Reinstall of pipelines via EasyBuild before running the pipeline.
- Estimated time: 4 days for 32 samples (10 trios, + 2 twins).
- 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.
- PH asks about LTS, AP JL and LM.
## 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, this Thursday.
- LM: Do we need other people (DICT, Leiden).
- Gained some enthusiasm from the admins in Groningen.
- No test-IDP at the UMCG.
- No test-IDP at the UMCG or LUMC.
## Ansible and Easybuild integration
- PN made an idempotent playbook, checking handlers now.
## Closing remarks
- LM will contact the Imaging WP about Ansible.
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- LM has contact with the Imaging WP about Ansible.
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