Merge branch 'cw-2098' into 'dev'

Add AWS demo url configuration

See merge request epi2melabs/workflows/wf-bacterial-genomes!64

CHANGELOG.md

@@ -1,28 +1,31 @@
 # 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).
 
 ## [unreleased]
 ### Added
 - `--isolates` parameter that will run the ResFinder tool on the final assembly to output antimicrobial resistance genes.
+- Configuration for running demo data in AWS
 ### Changed
 - Report is now created with `ezcharts`.
 
 ## [v0.2.13]
 ### Fixed
 - Rows with too few / too many columns in `medaka_models.tsv`.
 - Check sample sheet script.
+
 ### Changed
 - Now uses new `fastq_ingress` implementation.
 
 ## [v0.2.12]
 ### Fixed
 - Medaka models added to container
+
 ### Removed
 - QUAST
-  
+
 ## [v0.2.11]
 ### Changed
 - `--basecall_cfg` is now used to determine suitable Medaka model, alternatively provide the name of a model with `--medaka_consensus_model` and `--medaka_variant_model` to override automatic selection.
@@ -38,7 +41,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [v0.2.8]
 ### Changed
 - Output QUAST stats for reference and denovo based assembly
-  
+
 ## [v0.2.7]
 ### Changes
 - Replace QUAST with MetaQUAST
@@ -47,8 +50,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Tidy up presentation in report
 - `-profile conda` is no longer supported, users should use `-profile standard` (Docker) or `-profile singularity` instead
 - Docs update
+
 ### Added
 - `nextflow run epi2me-labs/wf-bacterial-genomes --version` will now print the workflow version number and exit
+
 ### Fixes
 - Prokka only runs in denovo assembly mode
 - Tidy up report code
@@ -57,6 +62,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changes
 - Added QUAST for assembly stats
 - Remove sanitize option
+
 ### Fixes
 - Update syntax to fix reference error
 
@@ -65,6 +71,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Better help text on cli
 - Fastqingress metadata map
 - Use groovy script to ping after workflow has run
+
 ### Fixes
 - Output medaka vcf
 - Remove reliance on simpleName
@@ -83,6 +90,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Visualisation of prokka output.
 - Choice of de novo assembly or alignment.
 - Supports multibarcodes
+
 ### Updated
 - Medaka version.
 - Depth coverage graphs.
@@ -92,6 +100,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 - Update project with latest practices from wf-template.
 - Use `mamba` by default when using conda profile.
+
 ### Fixed
 - Incorrect specification of conda environment file location.
 
@@ -114,12 +123,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [v0.1.0]
 ### Added
 - Prokka can be optionally run to annotate consensus sequence.
+
 ### Changed
 - Variant call summary produced using aplanat report component.
 
 ## [v0.0.1]
-
-Initial release
+- Initial release
 
 ### Added
 - Basic running of medaka variant calling and report.
+

nextflow_schema.json

@@ -4,6 +4,7 @@
     "title": "epi2me-labs/wf-bacterial-genomes",
     "description": "Assembly, variant calling, and annotation of bacterial genomes.",
     "demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-bacterial-genomes/wf-bacterial-genomes-demo.tar.gz",
+    "aws_demo_url": "https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-bacterial-genomes/wf-bacterial-genomes-demo/aws.nextflow.config",
     "url": "https://github.com/epi2me-labs/wf-bacterial-genomes",
     "type": "object",
     "definitions": {