nanopore container splits

JD2112 commented 8 months ago

The purpose of the code changes are as follows:

[x] nanopore container splits into nanopolish and medaka [x] fixed issues with nanopolish, added numpy (1.21.0) and tensorflow (1.14.0) [x] medaka version updated to 1.7.2 [x] --medaka-model added to medaka workflow. [x] README updated [ ] needs container updated on gms-Dockerhub.

Standard test procedure

[x] The self-test mentioned in the README finished successfully
[x] Produced files contain expected values
[ ] The code has been reviewed by @octocat

This version is a:

[ ] MAJOR - when you make incompatible API changes
[x] MINOR - when you add functionality in a backwards compatible manner
[ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

JD2112 commented 8 months ago

Structure looks sound. Not test running it. So anything related to that is outside the scope of the approval.

@sylvinite Thanks, true. I don't think it will pass the test run, since I don't know the meadka-model for the test dataset provided in nanopore data folder. Second, new docker containers need to push to gms-dockerhub. Shall I do it manually?

sylvinite commented 8 months ago

If you need to push extra images to dockerhub, feel free to. The more the merrier ;)

genomic-medicine-sweden / gms-artic