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.

v0.3.28

Fixed

• Fixed an error which was causing only a single sample to be processed, instead of all samples in the input FASTQ directory

v0.3.27

Added

• Configuration for running demo data in AWS

v0.3.26

Changed

• --basecall_cfg is now used to determine a suitable Medaka model, alternatively provide the name of a model with --medaka_variant_model to override automatic selection
• Update documentation

Fixed

• --report_detailed was causing an error in report generation, as it requires the telemetry JSON which the workflow is no longer using. This parameter has been removed (#79)