Update notes_2017_04_11.md

notes/wd/notes_2017_04_11.md

@@ -5,20 +5,10 @@ Mark Santcroos (MS), Pieter Neerincx (PN), Gerben van der Vries (GV),
 Roan Kanninga (RK). Henk-Jan Zilverberg (HZ), Niels Idsinga (NI)
 
 ## GoNL re-analysis
-Refset proposal:
 
-- PN and JL are going to send this to the NCBI.
-- The VKGL will be contacted for feedback.
-
-RK: We should enable base recalibration.
-
-- Can we use multiple recalibration files on the fly?
-- If so, compare to the 'polished BAM' method.
-
-QC:
-
-- BAM statistics.
-- Concordance with both array data and hg19-VCFs.
+GoNL spec
+- GoNL spec will be freezed by Thursday. - 
+- QUAL in VCF? New QUAL introduced by GATK. 
 
 ## eLAN
 Resolved.
@@ -33,8 +23,9 @@ PN, MS, GV, Paul van Dijk had a hands-on session.
 - PN wanted to have a test/acc instance of IDP at Groningen for testing. 
 
 ## Ansible and Easybuild integration
-Ansible installation testing:
-
-- GV succeeded installing easybuild via ansible on Shark.
+- 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 
+work around solution to see if it is reasonable. 
 
-## Virtual cluster setup at HPC Cloud (Mark)
\ No newline at end of file
+## Virtual cluster setup at HPC Cloud (MS)
\ No newline at end of file