v1.2.2

Changed

• Reconcile workflow with wf-template v5.2.6

v1.2.1

Changed

• Reconcile workflow with wf-template v5.2.5

v1.2.0

Added

• Logging to file for artic commands ({barcode}.artic.log.txt)
• --override_basecaller_cfg parameter for cases where automatic basecall model detection fails or users wish to override the automatic choice

Removed

• Unused nextclade_version parameter
• The --medaka_variant_model parameter as the appropriate Medaka model is now automatically determined from the input data
• The now redundant --basecaller_cfg parameter as its value is now automatically detected from the input data on a per-sample basis

Changed

• Reconciled workflow with wf-template v5.2.1
• Updated Medaka to v1.12.1

v1.1.0

Updated

• Nextclade updated to V3

Removed

• Nextclade V2 datasets

v1.0.0

Changes

• Documentation
• Defined resource requirments

v0.3.33

Changes

• Updates for cloud readiness
• Docs updated

Removed

• Default local executor CPU and RAM limits

v0.3.32

Fixed

• reporting of sequence summaries crashing with TypeError
• sed error when writing to tmp

v0.3.31

Changed

• --update_data default is now true to get latest lineage data from Pangolin and Nextclade

Updated

• Pangolin and Nextclade containers update to latest data

v0.3.30

Added

• New primer schemes; ARTIC V5.3.2 and Midnight IDT V2

Updated

• Nextclade bump to 2.14.0
• Pangolin bump to 4.3
• For alt primers we take the largest region (Updated ARTIC code merges a canonical primer site with an alt site, producing an interval that encompasses both)

v0.3.29

Changed

• Example command to use demo data.
• Updated GitHub issue templates to force capture of more information.
• Bumped minimum required Nextflow version to 22.10.8
• Enum choices are enumerated in the --help output.
• Enum choices are enumerated as part of the error message when a user has selected an invalid choice.
• Now uses hard-coded values instead of params.threads in fastqingress.