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broadinstitute / picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
https://broadinstitute.github.io/picard/
MIT License
974 stars 370 forks source link

Integration Testing #1592

Open nikellepetrillo opened 4 years ago

nikellepetrillo commented 4 years ago

Feature request

Description

The Lantern team wanted to see if integration tests were something people would be interested in having. I believe @yfarjoun proposed that we can use CARROT to do nightly or on-release tests instead of PR tests. Running on every PR may be too expensive with the number of commits that are made to Picard.

If there are any opinions or any other ideas on this issue we would love to hear them! cc @jessicaway @kbergin

kbergin commented 3 years ago

Here, we are proposing exploring more regular testing of some key tools in Picard releases by running the tools in standardized pipelines on different data types. We are motivated by the a recent effort to update our whole genome processing pipeline to a newer version of Picard. When testing this update, a few bugs in Picard were discovered i.e. 1589, 1581, 1571 (hopefully tagging the right PRs here).