Update notes_2017_04_11.md

notes/wd/notes_2017_04_11.md

 # Work discussion 11-04-2017
 
-Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
+Present: Jonathan Vis (JV), Leon Mei (LM), 
 Mark Santcroos (MS), Pieter Neerincx (PN), Gerben van der Vries (GV),
 Roan Kanninga (RK). Henk-Jan Zilverberg (HZ), Niels Idsinga (NI)
 
 ## GoNL re-analysis
-
-GoNL spec
-- GoNL spec will be freezed by Thursday. - 
-- QUAL in VCF? New QUAL introduced by GATK. 
+- RK started a version describing exact commands used for GoNL pipeline. PH already provided his input.
+- GoNL spec will be freezed by Thursday.
+- RK asked about if we should use the new QUAL option in GATK (by default off in GATK 3.7 but on in GATK 4.0). Our current proposal is to use it and test it based on GIB's high confidence variant calls.
 
 ## eLAN
 Resolved.
 
 ## CoManage
-PN, MS, GV, Paul van Dijk had a hands-on session.
-
 - HZ has LDAP server up running at Groningen site. They are waiting for the CoManage instance at SURF. 
-- MS commented that we can log in to CoManage now (PN should have details). But still has problems getting it running. MS suggested to contact Gerben (SURFSara) for support.
-- Communication to Gerben (SURFSara) should be CCed between LUMC and Groningen teams. NI will try configuration tomorrow
-- We don't have problems with the SQL database anymore.
-- PN wanted to have a test/acc instance of IDP at Groningen for testing. 
+- MS commented that we can log in to CoManage now (PN should have details). But MS still has problems getting it running properly. MS suggested to contact Gerben (SURFSara) for support.
+- Communication to Gerben (SURFSara) should be copied with both LUMC and Groningen teams. NI will try configuration tomorrow.
+- We don't have problems with the SQL database used for CoManage at SURF anymore.
+- PN wanted to have a test/acceptance instance of IDP at Groningen for testing. 
 
 ## Ansible and Easybuild integration
-- Gerben fixed the Molgenis-compute evn. Currently deployed at the home dir of Gerben. GV will deploy the env at bbmri-nl share.
-- Pieter is improving the ansible playbook (replacing wget in shell with native Ansible commands).
-- Pieter brought up an Ansible issue he encountered. Work around now by sourcing (e.g., bashrc) in Ansible. Because login shells of Ansible are not interactive. MS will check PN's 
+- GV fixed the Molgenis-compute env. Currently deployed at the home dir of GV. GV will deploy the env at bbmri-nl share.
+- PN is improving the ansible playbook (e.g., replacing wget in shell with native Ansible commands). Available at bbmri-nl github.
+- PN had an Ansible issue. Login shells of Ansible are not interactive, so current work around is to sourcing (e.g., bashrc) explicitly in Ansible.  MS will check PN's 
 work around solution to see if it is reasonable. 
-
-## Virtual cluster setup at HPC Cloud (MS)
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