Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Launch proviral pipeline #706

Closed
6 tasks done
donkirkby opened this issue Apr 20, 2021 · 0 comments
Closed
6 tasks done

Launch proviral pipeline #706

donkirkby opened this issue Apr 20, 2021 · 0 comments
Labels
enhancement
Milestone
7.15 - HIVdb 9.0

Comments

@donkirkby
Copy link
Member

donkirkby commented Apr 20, 2021 •
edited
Loading

When a sample's project code is NFLHIVDNA, launch the proviral pipeline.

  • Add proviral pipeline type, and launch it after denovo main run finishes.
  • Add cascade.csv input.
  • Add run folder name to sample info file, and pass it as input to proviral pipeline.
  • Only add sample column if it's not already there during collation.
  • Don't keep collating proviral results when denovo samples aren't finished.
  • Also download files from hivseqinr_0/Results_Final.
@donkirkby donkirkby added this to the 7.14 - Primers by Project milestone Apr 20, 2021
donkirkby added a commit that referenced this issue Apr 21, 2021
@donkirkby
Pass sample_info.csv to Proviral pipeline for #706.
197ead3 
Also check before adding sample column when collating files.
donkirkby added a commit that referenced this issue Apr 21, 2021
@donkirkby
Download proviral outputs for #706.
e2a0375
donkirkby added a commit that referenced this issue Apr 21, 2021
@donkirkby
Fix broken test by checking for empty files for #706.
05d66f7
donkirkby added a commit that referenced this issue Apr 21, 2021
@donkirkby
Add run name to sample_info.csv for #706.
92ac782
donkirkby added a commit that referenced this issue Apr 22, 2021
@donkirkby
Don't collate proviral results until denovo results are done, for #706.
28dd11b
donkirkby added a commit that referenced this issue May 5, 2021
@donkirkby
Download HIVSeqinR working folder, for #706.
f849241
donkirkby added a commit that referenced this issue May 5, 2021
@donkirkby
Add parent folder before unpacking HIVSeqinR working files, as part of …
7891db2 
…#706.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
enhancement
Projects
None yet
Milestone
7.15 - HIVdb 9.0
Development

No branches or pull requests
1 participant
@donkirkby