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

Setup CI for exome variant pipeline #238

Closed
jvivian opened this issue Apr 18, 2016 · 4 comments
Closed

Setup CI for exome variant pipeline #238

jvivian opened this issue Apr 18, 2016 · 4 comments
Assignees
@jvivian
Labels
enhancement

Comments

@jvivian
Copy link
Collaborator

jvivian commented Apr 18, 2016 •
edited by hannes-ucsc
Loading

No description provided.

@jvivian jvivian self-assigned this Apr 18, 2016
@jvivian jvivian mentioned this issue Apr 18, 2016
Closed
@hannes-ucsc hannes-ucsc changed the title Setup CI for Exome Variant Pipeline Setup CI for exome variant pipeline Apr 18, 2016
@jvivian
Copy link
Collaborator Author

jvivian commented Apr 19, 2016

Waiting on Tumor/Normal test inputs from @jpfeil

@hannes-ucsc
Copy link
Contributor

Blocked on BD2KGenomics/protect#6

@jvivian
Copy link
Collaborator Author

jvivian commented May 16, 2016

@jpfeil Where are the reads you used for the tumor / normal samples you implemented in the ProTect CI?

@jpfeil
Copy link
Contributor

jpfeil commented May 16, 2016

pimmuno-test-data/CI_test_input/reads/

Normal DNA: ERR01639X_HCC1954BL.chr6.1.fq.gz
Tumor DNA: ERR01636X_HCC1954.chr6.1.fq.gz

Here is a link to the SRA page:
http://www.ncbi.nlm.nih.gov/sra/?term=ERR016361

@jvivian jvivian added in progress and removed ready labels May 18, 2016
jvivian added a commit that referenced this issue May 28, 2016
@jvivian
Refactor exome pipeline (resolves #270, resolves #238, resolves #276, r…
22b80fe 
…esolves #282, resolves #279, resolves #284, resolves #274)
jvivian added a commit that referenced this issue May 28, 2016
@jvivian
Refactor exome pipeline (resolves #270, resolves #238, resolves #276, r…
ec74407 
…esolves #282, resolves #279, resolves #284, resolves #274)
hannes-ucsc added a commit that referenced this issue May 31, 2016
@hannes-ucsc
Merge pull request #286 from /issues/270-refactor-variant-pipeline-to…
0f7b0a3 
…-use-config

Refactor exome pipeline (resolves #270, resolves #238, resolves #276,…
jpfeil pushed a commit that referenced this issue Jun 3, 2016
@jvivian @jpfeil
Refactor exome pipeline (resolves #270, resolves #238, resolves #276, r…
adf8e67 
…esolves #282, resolves #279, resolves #284, resolves #274)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@jvivian jvivian

Labels
enhancement
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@hannes-ucsc @jvivian @jpfeil