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Add AWS demo url configuration

See merge request epi2melabs/workflows/wf-artic!135
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@mattdmem
mattdmem committed May 16, 2023
2 parents b0566cb + 79651a6 commit 185c6a7
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56 changes: 36 additions & 20 deletions 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](https://keepachangelog.com/en/1.0.0/),
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [v0.3.26]
Expand All @@ -12,6 +12,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### 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 (https://github.com/epi2me-labs/wf-artic/issues/79)

### Added
- Configuration for running demo data in AWS

## [v0.3.25]
### Updated
- Implemented new fastqingress
Expand All @@ -25,8 +28,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [v0.3.23]
### Changed
- medaka bumped to 1.7.2 (np-artic bump to 1.3.0_19)

### Added
- medaka models for kit14 - R10.4.1

### Fixed
- scheme directory bug in labs/windows (https://github.com/epi2me-labs/wf-artic/issues/73)

Expand All @@ -35,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- workflow-glue python psuedo package
- pangolin to 4.2
- nextclade to 2.11.0

### Removed
- spike-seq primer schemes
- telemtry generation
Expand All @@ -54,6 +60,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Documentation
- pangolin to 4.1.3
- nextclade to 2.8.0

### Fixed
- Metadata map handling

Expand All @@ -71,12 +78,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### 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

Expand All @@ -89,19 +98,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- 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
- 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`
Expand All @@ -116,6 +124,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- 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
Expand Down Expand Up @@ -155,6 +164,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- 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.

Expand All @@ -165,6 +175,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- 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

Expand All @@ -179,38 +190,41 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### 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.
- 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.
- 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.
Expand All @@ -223,10 +237,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [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.
- 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.
Expand All @@ -249,6 +264,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [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.
Expand All @@ -257,6 +273,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [v0.1.2]
### Fixed
- Recovery after `artic minion` fails.

### Added
- Report item detailing failed analyses.

Expand Down Expand Up @@ -287,6 +304,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### 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
Expand All @@ -303,20 +321,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [v0.0.3]
### Changed
- Automatically select min/max read lengths base on scheme.
###
### Added
- Added command-line argument validation.

## [v0.0.2]

Automation release
* Automation release

### Added
- Continuous deployment.


## [v0.0.1]

Initial release
* Initial release

### Added
- Basic running of Artic workflow and reporting.

1 change: 1 addition & 0 deletions nextflow_schema.json
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"title": "epi2me-labs/wf-artic",
"description": "Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.",
"demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-artic/wf-artic-demo.tar.gz",
"aws_demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-artic/wf-artic-demo/aws.nextflow.config",
"url": "https://github.com/epi2me-labs/wf-artic",
"type": "object",
"definitions": {
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