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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[v0.3.19]

Changed

  • Fastqingress metadata map
  • Nextclade < v2.0.0 no longer supported
  • Documentation
  • pangolin to 4.1.3
  • nextclade to 2.8.0

Fixed

  • Metadata map handling

[v0.3.18]

Changes

  • pangolin to v4.1.1
  • nextclade data updated

[v0.3.17]

Changes

  • Args parser for fastqingress
  • Set out_dir option type to ensure output is written to correct directory on Windows

[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 epi2me-labs#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 epi2me-labs#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

[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_detailed 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.
  • Output artic.json.

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

[v0.3.1]

Added

  • Per-sample bam files now published to output directory.

Changed

  • Data ingress now performed by standard module.

[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.

[v0.2.0]

Added

  • Ability to configure depth coverage reporting value.
  • Add explicit pins of conda packages.
  • Inclusion of SpikeSeq workflow, and reporting.
  • Optional auto-detection of sample_id

[v0.1.4]

Changed

  • Improved display of coverage traces in report.

[v0.1.3]

Added

  • Check format of sample sheet before executing main workflow.

Fixed

  • Parsing of V1200 .bed file for nextclade report.
  • Empty barcode directories are ignored.
  • Nextclade report component upgraded to better handle poor data.

[v0.1.2]

Fixed

  • Recovery after artic minion fails.

Added

  • Report item detailing failed analyses.

[v0.1.1]

Fixed

  • Correct value of wfversion in config.
  • Processing of single sample inputs.

[v0.1.0]

Added

  • Added variant call summary section to report.

[v0.0.9]

Changed

  • Moved scripting to bin directory.

[v0.0.8]

Fixed

  • Fix lack of help message when --help run.

[v0.0.7]

Changed

  • Sample sheet is no longer required.
  • Sort report items consistently by sample name.
  • Nextclade visual will display overlap to primer scheme selected by user.

[v0.0.6]

Added

  • Support for fragmented amplicons.
  • Enabled use of conda profile.

Changed

  • Use custom np-artic package based on 1.3.0-dev branch of original.
  • Use nextclade from conda package
  • Amended default local executor CPU resource to be more parsimonious.

[v0.0.5]

Changed

  • Amended report text

[v0.0.4]

Changed

  • Discretize coverage plots for speed

[v0.0.3]

Changed

  • Automatically select min/max read lengths base on scheme.

  • Added command-line argument validation.

[v0.0.2]

Automation release

Added

  • Continuous deployment.

[v0.0.1]

Initial release

Added

  • Basic running of Artic workflow and reporting.