Xref Mapping New pipeline

[TamaraNaboulsi]

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Requirements

• Filling out the template is required.
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • if you change the schema you must patch the test databases as well, see Updating the schema
  • the PR must not fail unit testing

Description

New xref mapping pipeline written in Nextflow and python, as well as fixes and improvement to the download pipeline.

Use case

This PR contains the next step of the xref refactoring and rewriting using Nextflow and python, which started with the download part and now the mapping part. The general flow of the pipeline is still the same. Various improvements and fixes for long-standing issues have been added. In addition, a test suite was added, though it doesn't cover every module yet. The Confluence page for the new xref pipelines has been updated.

The new pipeline has been tested on multiple vertebrate and plant species, both independently and together, and is working as expected. It has also been tested with human and mouse (along with the modified download pipeline for gencode), though few issues are still being checked.

Benefits

New pipeline with new technologies.

Possible Drawbacks

Refer to "Known Issues" section in Confluence page.

Testing

• Have you added/modified unit tests to test the changes?
• If so, do the tests pass?
• Have you run the entire test suite and no regression was detected?
• TravisCI passed on your branch

Dependencies

If applicable, define what code dependencies were added and/or updated.