[x] Determine how to best generate freeze list (white or maybe black)
possibly writing entirely new GDCtool for suchTCGA FFPE samples should be culled
[x] Invite FC team member to lab meeting?
[x] Outline workshop demo SOP for others to run
[x] Each user should construct a cohort to analyze: from GDC HG38 TCGA data
. we will walk through how to generate the cohort list: using new filepaths api
. our example will default to using full cohort(s)
. but users can feel free to remove unwanted samples before feeding to *_new scripts
. OR specify --blacklist or --whitelist flag to new gdac_freeze tool
output of this new filepaths API needs to be filtered to generate participant list & sset definition
[x] Write talk
[x] review issues in various repos, to smooth out rough edges that may hinder new SOP users: e.g.
[x] more importantly, gdac_dashboard should NOT use ssh to retrieve DOT files used to prune the submissions reflected in the table, to reduce amount of user configuration, ssh password setup etc
David:
[x] mainly work on stddata_new and analyses_new tools
[x] add details to SOP demo outline
. copy AWG gqueues template to google doc & make commentable by all
. give working example of editing SSET definition, to create subtype/etc sample list for run: this means taking SSET that is output from gdac_freeze tool and removing some lines
[x] accept whitelist (and black, if possible to do in time, but not the first priority); *DONE BY MIKE
[x] think about how to unique-ify workspace names, since many people will be running SOP at once
Mike:
possibly writing entirely new GDCtool for suchTCGA FFPE samples should be culledInvite FC team member to lab meeting?Outline workshop demo SOP for others to runoutput of this new filepaths API needs to be filtered to generate participant list & sset definitionmore importantly, gdac_dashboard should NOT use ssh to retrieve DOT files used to prune the submissions reflected in the table, to reduce amount of user configuration, ssh password setup etcDavid:
accept whitelist (and black, if possible to do in time, but not the first priority); *DONE BY MIKE