v0.3.7

Fixed

• Pangolin update step now checks for internet connection

v0.3.6

Changes

• Pangolin updated to 3.1.16 (Will now call B.1.1.529 successfully)
• Pangolin now auto updates before it runs (internet connectivity required)
• Nextclade updated to 1.5.1

Fixed

• Segmentation faults in artic-tools vcfcheck code.

v0.3.5

Added

• Error report if no data at all.
• Telemetry JSON.
• Nextclade errors output as seperate table.
• --report_debug flag to show additional coverage plots
• Parsing of sample sheet to include a type column

Changes

• sample_name changed to sample_id throughout

v0.3.4

Added

• Option to add suffix to HTML report name.
• Error message if fastq input file evaluates to null.
• Output Nextflow schema JSON file.
• Output artic JSON file.

v0.3.3

Changed

• Update nextclade to c++ version 1.3.0, install via bioconda.
• Update aplanat to v0.5.4.

Added

• V4.1 primer set for spike-seq.
• Tag for pangolin image is now specified in nextflow config.
• Integrate max_softclip_length parameter to be passed into artic minion.

Fixed

• Parsing of sample_name column from summary files during report curation.

v0.3.2

Changed

• Updated fastcat and aplanat versions for standardised software version
  reporting.

Fixed

• Empty GVCF file not produced when ARTIC failed.
• conda environment file location incorrectly specified in nextflow.config

v0.3.0

Fixed

• Updated medaka to v1.4.3 for model pre-download.
• Work around issue where pyvcf writes QUAL values as '.' and not 0.

Changed

• Removed the autodetect sample_id option for now.
• Updated default model to be a variant calling one. Although labelled as
  PromethION specific (_prom in name), this model should be preferred
  on all platforms of non-variant (consensus) platform specific models.
• Derive software versions from CLI rather than conda list.

Added

• Field alias in sample sheet CSV serves as alternative to sample_name.
• Added V4 primerscheme to data directory.

v0.2.3

Changed

• Updated medaka to v1.4.2.
• Updated aplanat to v0.4.0.

v0.2.2

Added

• Added summary of software parameters section to report

Changed

• genotype_variants option can now be used without specifying a path, falling
  back to the scheme default, if one exists.
• Removed vestigial spike-seq scheme versions

Fixed

• Updated allVariants step to normalise REF fields to fix vcf merge issue
• Prevented nextclade from using all available threads

v0.2.1

Fixed

• Intermittent error producing genotyping summary