Release v2.1.0

• Fix #12 by improving custom scheme behaviour

Full Changelog: 2.0.0...2.1.0

Release v2.0.0

Some fairly major changes to the pipeline, primer schemes are no longer packaged with the pipeline but are pulled from the https://github.com/quick-lab/primerschemes repository, from a user perspective this will not change much though.

Reference selection functionality is now supported! For the artic-inrb-mpox scheme the pipeline will try to select which reference sequence is most appropriate for each of your sequencing barcodes so don't be surprised if you end up with output FASTAs with slightly different co-ordinates, this just means that they belong to different clades.

What's Changed

• fix sample sheet csv header by @ammaraziz in #9
• Refactor to allow reference selection functionality by @BioWilko in #11

New Contributors

• @ammaraziz made their first contribution in #9

Full Changelog: 1.2.8...2.0.0

Release v1.2.8

Updated squirrel version from 1.0.10 to 1.0.12

What's Changed

• Update squirrel version by @rmcolq in #8

Release v1.2.7

Full Changelog: 1.2.6...1.2.7

Release v1.2.6

Explicitly grab amd64 docker containers until arm container becomes available

Full Changelog: 1.2.5...1.2.6

Release v1.2.5

Add conda / mamba profiles to the pipeline

What's Changed

• Add conda / mamba profiles by @BioWilko in #7

Full Changelog: 1.2.4...1.2.5

Release v1.2.4

Bump fieldbioinformatics container version

Full Changelog: 1.2.3...1.2.4

Release v1.2.3

Fix minor bug with custom scheme declaration

Full Changelog: 1.2.2...1.2.3

Release v1.2.2

Bump container version to 1.5.0

Full Changelog: 1.2.1...1.2.2

Release v1.2.1

Release 1.2.1

• Update fieldbioinformatics container version to fix bug in variant filtering

Full Changelog: 1.2.0...1.2.1