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

kraken pipe mini-fix #841

Merged

dpark01 merged 2 commits into master from dp-kraken-pipe

Jul 9, 2018

Member

dpark01 commented Jul 9, 2018

kraken.pipeline utilizes a background Picard process to pipe SamToFastq output into kraken. Nothing was waiting for this background process to terminate, and nothing was checking its error code for success or failure. This PR fixes both of those issues. Might possibly fix Non-deterministic failure of test_kraken_multi teardown #839 (though not 100% sure about that).
s/gzip/pigz/g in kraken reads output.

dpark01 added 2 commits

July 9, 2018 09:05


kraken: wait for Picard SamToFastq background process to finish befor…

b287af2

…e exiting, and also add error checking for background process.


fix syntax error

d4ab142

tomkinsc approved these changes

View reviewed changes

dpark01 merged commit 25d74fd into master

dpark01 deleted the dp-kraken-pipe branch

July 9, 2018 18:22

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment