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.
- Logging to file for artic commands (
{barcode}.artic.log.txt) --override_basecaller_cfgparameter for cases where automatic basecall model detection fails or users wish to override the automatic choice
- Unused
nextclade_versionparameter - The
--medaka_variant_modelparameter as the appropriate Medaka model is now automatically determined from the input data - The now redundant
--basecaller_cfgparameter as its value is now automatically detected from the input data on a per-sample basis
- Reconciled workflow with wf-template v5.2.1
- Updated Medaka to v1.12.1
- Nextclade updated to V3
- Nextclade V2 datasets
- Documentation
- Defined resource requirments
- Updates for cloud readiness
- Docs updated
- Default local executor CPU and RAM limits
- reporting of sequence summaries crashing with
TypeError - sed error when writing to tmp
--update_datadefault is nowtrueto get latest lineage data from Pangolin and Nextclade
- Pangolin and Nextclade containers update to latest data
- New primer schemes; ARTIC V5.3.2 and Midnight IDT V2
- 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)
- 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
--helpoutput. - 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.threadsinfastqingress.
- Fixed an error which was causing only a single sample to be processed, instead of all samples in the input FASTQ directory
- Configuration for running demo data in AWS
--basecall_cfgis now used to determine a suitable Medaka model, alternatively provide the name of a model with--medaka_variant_modelto override automatic selection- Update documentation
--report_detailedwas causing an error in report generation, as it requires the telemetry JSON which the workflow is no longer using. This parameter has been removed (epi2me-labs#79)
- Configuration for running demo data in AWS
- Implemented new fastqingress
- aplanat bumped to v0.6.16 to fix nextclade sequence view
- Updated to Oxford Nanopore Technologies PLC. Public License
- Custom primer schemes
- medaka bumped to 1.7.2 (np-artic bump to 1.3.0_19)
- medaka models for kit14 - R10.4.1
- scheme directory bug in labs/windows (epi2me-labs#73)
- workflow-glue python psuedo package
- pangolin to 4.2
- nextclade to 2.11.0
- spike-seq primer schemes
- telemtry generation
- Updated sample sheet to expect a file
- Updated description in manifest
- Fastqingress metadata map
- Nextclade < v2.0.0 no longer supported
- Documentation
- pangolin to 4.1.3
- nextclade to 2.8.0
- Metadata map handling
- pangolin to v4.1.1
- nextclade data updated
- Args parser for fastqingress
- Set out_dir option type to ensure output is written to correct directory on Windows
--pangolin_optionscommand line arg, use with quotes i.e.: "--analysis-mode fast"- NEB VarSkip V2b primer scheme added
- Better help text on cli
nextflow_schema.jsondefault primer scheme fix
- New docs format
- Issue with custom schemes
- 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
- 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
- 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
- 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
- Pangolin build fix
- NEB VarSkip V2 bed file now corrected
- Nextclade execution options changed as suggested in epi2me-labs#35
- Fixing
--samplesin schema
--samplesnow changed to--sampleand--sample_sheetintroduced- 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_versionand--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=1frompool=0
- Pangolin update now takes place at build stage, rather than during run
- Nextclade data was out of date, now calls Omicron
- Pangolin update step now checks for internet connection
- 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
- Segmentation faults in artic-tools vcfcheck code.
- Error report if no data at all.
- Telemetry JSON.
- Nextclade errors output as seperate table.
--report_detailedflag to show additional coverage plots- Parsing of sample sheet to include a
typecolumn
sample_namechanged tosample_idthroughout
- 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.
- Update nextclade to c++ version 1.3.0, install via bioconda.
- Update aplanat to v0.5.4.
- 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.
- Parsing of sample_name column from summary files during report curation.
- Updated
fastcatandaplanatversions for standardised software version reporting.
- Empty GVCF file not produced when ARTIC failed.
condaenvironment file location incorrectly specified innextflow.config
- Per-sample bam files now published to output directory.
- Data ingress now performed by standard module.
- Updated medaka to v1.4.3 for model pre-download.
- Work around issue where pyvcf writes QUAL values as '.' and not 0.
- Removed the autodetect sample_id option for now.
- Updated default model to be a variant calling one. Although labelled as PromethION specific (
_promin 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.
- Field
aliasin sample sheet CSV serves as alternative tosample_name. - Added V4 primerscheme to data directory.
- Updated medaka to v1.4.2.
- Updated aplanat to v0.4.0.
- Added summary of software parameters section to report.
- 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.
- Updated allVariants step to normalise REF fields to fix vcf merge issue.
- Prevented nextclade from using all available threads.
- Intermittent error producing genotyping summary.
- 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
- Improved display of coverage traces in report.
- Check format of sample sheet before executing main workflow.
- Parsing of V1200 .bed file for nextclade report.
- Empty barcode directories are ignored.
- Nextclade report component upgraded to better handle poor data.
- Recovery after
artic minionfails.
- Report item detailing failed analyses.
- Correct value of wfversion in config.
- Processing of single sample inputs.
- Added variant call summary section to report.
- Moved scripting to bin directory.
- Fix lack of help message when
--helprun.
- Sample sheet is no longer required.
- Sort report items consistently by sample name.
- Nextclade visual will display overlap to primer scheme selected by user.
- Support for fragmented amplicons.
- Enabled use of conda profile.
- 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.
- Amended report text
- Discretize coverage plots for speed
- Automatically select min/max read lengths base on scheme.
- Added command-line argument validation.
- Automation release
- Continuous deployment.
- Initial release
- Basic running of Artic workflow and reporting.