[Documentation] Refresh user guide
For the entire Arvados user guide, look for documentation that is out-of-date, and prepare a branch that brings those parts up-to-date.
The tutorial pages are specifically a priority. Please actually follow their steps to make sure that it all works, and that sample outputs you get reasonably match what's documented. Any mismatches there are candidates for updating.
Merge branch '7015-remove-pipeline-instance-from-recursive-arv-copy-doc'
#7 Updated by Bryan Cosca over 4 years ago
Updated http://doc.arvados.org/user/tutorials/running-external-program.html with more escapes in the bwa read group -- https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-iwjstz139qzrkdq
#9 Updated by Bryan Cosca over 4 years ago
branch 7015-update-user-guide is up for review on c31abb
I went through the entire user guide and either filed bugs on things that didn't work as expected (attached to the this ticket) or fixed the documentation. I'm not sure what else I can do here, its possible I missed some things but I tried to do a thorough read/test of everything.
I made sure the Develop a new pipeline section works as extended as specified in the description. I made one change in note #7 that I think people were running into.
#10 Updated by Brett Smith over 4 years ago
Bryan Cosca wrote:
I went through the entire user guide and either filed bugs on things that didn't work as expected (attached to the this ticket)…
Thanks. I'm going to break these off the ticket so that we can track them through Redmine backlogs, and make sure they get addressed appropriately. I'll add relationships so we remember where they came from, though.
#12 Updated by Nico César over 4 years ago
doc/user/index.html.textile.liquid line 13 has an extra space at the end. delete it before merging.
there changes aren't that big. and LGTM...
I trust that the triple escape "\\\" is OK in doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid:
- "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id", + "@RG\\\tID:group_id\\\tPL:illumina\\\tSM:sample_id",
ready for merge in my opinion