v0.3.18

Changes

• pangolin to v4.1.1
• nextclade data updated

v0.3.16

Added

• --pangolin_options command line arg, use with quotes i.e.: "--analysis-mode fast"
• NEB VarSkip V2b primer scheme added

Changes

• Better help text on cli

v0.3.15

Fixed

• nextflow_schema.json default primer scheme fix

Changes

• New docs format

v0.3.14

Fixed

• Issue with custom schemes

v0.3.13

Changes

• Updated primer schemes
• Removed scheme downloading from np-artic
• V1200 Midnight naming changed:
  • v1 of the kit (MRT.001.10) is called Midnight-ONT/V1
  • v2 of the kit (MRT.001.20) is called Midnight-ONT/V2
  • v3 of the kit (MRT.001.30) is called Midnight-ONT/V3
    • It should be noted that primer 21_RIGHT only has one record in the bed, to represent
      the maximum possible region covered by the right primers for this amplicon
• pangolin bumped to 4.0.5
• nextclade bumped to 1.11.0

Added

• Ability to specify custom primers with --custom_scheme
  • --min_len and --max_len must be specified when using this option
• --list_schemes option that lists available schemes and quits the workflow

v0.3.12

Changes

• Updated medaka default model to r941_min_hac_variant_g507
• Nextclade bumped to 1.10.3
• Help text for sample sheets updated as suggested in #41
• Output a combined depth file for later analysis

v0.3.11

Changes

• Nextclade data is now checked for compatibility with Nextclade version
• Normalise no longer hardcoded
• Nextclade bump to 1.10.2
• Nextclade data to 2022-02-07T12:00:00Z
• Pangolin bump to 3.1.20

Fixed

• Pangolin build fix
• NEB VarSkip V2 bed file now corrected
• Nextclade execution options changed as suggested in #35
• Fixing --samples in schema

v0.3.10

Changes

• --samples now changed to --sample and --sample_sheet introduced
• Schema updated to allow integration with epi2me services
• Added ARTIC V4.1 primer set
• Added NEB VarSkip primer sets
• Updated Nextclade data to 2022-01-05T19:54:31Z
• Updated Nextclade to v1.8.0
• Updated pangolin to v3.1.17
• Now outputs all sample VCFs as well as merged VCF
• Pangolin and Nextclade versions can be specified at runtime --pangolin_version and --nextclade_version
• Pangolin and Nextclade data can be updated at runtime with --update_data
• All Nextclade data versions included in repo for user selection with --nextclade_data_tag, most recent will be used by default
• Updated max-length of amplicons for NEB long
• Updated NEB-v1a-long bed file to pool=1 from pool=0

v0.3.9

Changes

• Pangolin update now takes place at build stage, rather than during run

v0.3.8

Fixed

• Nextclade data was out of date, now calls Omicron