Merge pull request #52 from phac-nml/bump-version

bumped version

Author: mattheww95

CHANGELOG.md

@@ -1,35 +1,37 @@
-# mk-kondo/mikrokondo: Changelog
+# phac-nml/mikrokondo: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.0dev - [date]
+## v0.1.0 - [2024-03-22]
 
-Initial release of mk-kondo/mikrokondo, created with the [nf-core](https://nf-co.re/) template.
+Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trimming and quality control, contamination detection, assembly (isolate, metagenomic or hybrid), annotation, AMR detection and subtyping of genomic sequencing data targeting bacterial or metagenomic data.
 
-### `Added`
+- Bumped version number to 0.1.0
+
+- Updated docs to include awesome-page plugin and restructured readme. 
 
-Updated docs to include awesome-page plugin and restructured readme. 
+- Updated coverage defaults for Shigella, Escherichia and Vibrio
 
-Updated coverage defaults for Shigella, Escherichia and Vibrio
+- Updated file outputs to match the nf-iridanext plug-in
 
-Updated file outputs to match the nf-iridanext plug-in
+- Incorporated IRIDANext plug-in
 
-Incorporated IRIDANext plug-in
+- Upgraded nf-validation to latest version 2.0.0
 
-Upgraded nf-validation to latest version 2.0.0
+- Added message to final summary report notifying user if an assembly does not have any contigs exceeding the minimum contig length parameter
 
-Added message to final summary report notifying user if an assembly does not have any contigs exceeding the minimum contig length parameter
+- Added contig count check before running Quast to ensure empty files are not passed in.
 
-Added contig count check before running Quast to ensure empty files are not passed in.
+- Added process to filter contigs based on a minimum required contig length.
 
-Added process to filter contigs based on a minimum required contig length.
+- Added option to force sample to be implemented as an isolate
 
-Added option to force sample to be implemented as an isolate
+- Changed salmonella default default coverage to 40
 
-Changed salmonella default default coverage to 40
+- Added integration testing using [nf-test](https://www.nf-test.com/).
 
-Added integration testing using [nf-test](https://www.nf-test.com/).
+### `Added`
 
 ### `Fixed`
 

README.md

@@ -174,6 +174,8 @@ Add `--profile singularity` to switch from using docker by default to using sing
 
 ## Troubleshooting and FAQs:
 
+Within release 0.1.0, Bakta is currently skipped however it can be enabled from the command line or within the nextflow.config (please check the docs for more information). It has been disabled by default due issues in using the latest bakta database releases due to an issue with `amr_finder` there are fixes available and older databases still work however they have not been tested. A user can still enable Bakta themselves or fix the database. More information is provided here: https://github.com/oschwengers/bakta/issues/268 
+
 For a list of common issues or errors and their solutions, please read our [FAQ section](https://phac-nml.github.io/mikrokondo/troubleshooting/FAQ/).
 
 ## References

nextflow.config

@@ -53,7 +53,7 @@ params {
     skip_raw_read_metrics = false
     skip_version_gathering = false
     skip_subtyping = false
-    skip_bakta = false
+    skip_bakta = true
     skip_abricate = false
     skip_checkm = false
     skip_depth_sampling = false // TODO have it mentioned that this should be turned off for metagenomic runs
@@ -1026,7 +1026,7 @@ manifest {
     description     = """Mikrokondo beta"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
+    version         = '0.1.0'
     doi             = ''
 }
 

nextflow_schema.json

@@ -355,6 +355,7 @@
                 },
                 "skip_bakta": {
                     "type": "boolean",
+		    "default": true,
                     "description": "Skip annotation with Bakta"
                 },
                 "skip_abricate": {
@@ -572,4 +573,4 @@
             "$ref": "#/definitions/other"
         }
     ]
-}
+}