3.1.1

This version is UNSTABLE and DEPRECATED.
This release tags the WDL imports to a specific version.

4.0.0-alpha

What's Changed

• Fix contamination list extension by @adthrasher in #30
• Updated DX app for multiple mappers and references. Add memory requir… by @adthrasher in #29
• Combine tie bams and contam lists. Point WDL workflows to GitHub container registry. by @adthrasher in #31
• Commit missing CWL script by @adthrasher in #32
• Remove docker tag check from master. by @adthrasher in #34
• Bump action version. Update for master->main. by @adthrasher in #36
• Point to updated STAR release by @adthrasher in #37

Full Changelog: 3.1.4...4.0.0-alpha

3.1.4

This release updates the WDL workflows to point to the latest changes.

3.1.3

TweakSam dependency has been updated to eliminate Picard validation errors. The MC tag is now removed from records when XenoCP sets the read to unmapped.

3.1.2

Bump WDL files imported from stjudecloud/workflows to v3.0.0.

3.1.0

This version is UNSTABLE and DEPRECATED.
This version introduces a WDL workflow implementation of XenoCP.

v3.0.0

Readme and license (#7)

* Initial cleanups on top sections of readme

Everything starting with the Building header still needs to be cleaned
up.

* Cleaning up the quickstart and updating sample data configs.

* Restructure README and add evaluation of sample data

* Adding license information and seeking help

* updating paths for build output

* Updating gradle install command

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Apply suggestions from code review

Co-Authored-By: Michael Macias <michael.macias@stjude.org>

* Update README.md

* Update DNAnexus app to use the input file name prefix.

* Update view_awk_picard.sh to call awk directly to get around limitations on using the shebang with env to find awk and run with arguments.