From 46382bfcc9b19d60e15be3ef175abe1b602ec100 Mon Sep 17 00:00:00 2001
From: ryanjameskennedy <ryanjameskennedy@icloud.com>
Date: Thu, 29 Aug 2024 13:04:08 +0200
Subject: [PATCH] Update to v0.9.0

---
 CHANGELOG.md                   |  8 ++++++++
 configs/nextflow.base.config   |  2 +-
 configs/nextflow.ci.config     |  2 +-
 configs/nextflow.dev.config    |  2 +-
 configs/nextflow.hopper.config | 12 ++++++------
 configs/nextflow.ngp.config    |  2 +-
 6 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1ed7b595..100f7663 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+### Fixed
+
+### Changed
+
+## [0.9.0]
+
+### Added
+
 - Added long-read test data (S. aureus)
 - Added `samplelist_nanopore.csv` for running long-read test data
 - Added location of documentation to `README` 
diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
index e2cbb770..47934a6c 100644
--- a/configs/nextflow.base.config
+++ b/configs/nextflow.base.config
@@ -313,5 +313,5 @@ manifest {
 	homePage = 'https://github.com/genomic-medicine-sweden/jasen'
 	description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes'
 	mainScript = 'main.nf'
-	version = '0.8.0'
+	version = '0.9.0'
 }
diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
index 1c416a29..f5722c53 100644
--- a/configs/nextflow.ci.config
+++ b/configs/nextflow.ci.config
@@ -296,5 +296,5 @@ manifest {
 	homePage = 'https://github.com/genomic-medicine-sweden/jasen'
 	description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes'
 	mainScript = 'main.nf'
-	version = '0.8.0'
+	version = '0.9.0'
 }
diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config
index 1b2ef0fb..375a9ec0 100644
--- a/configs/nextflow.dev.config
+++ b/configs/nextflow.dev.config
@@ -296,5 +296,5 @@ manifest {
 	homePage = 'https://github.com/genomic-medicine-sweden/jasen'
 	description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes'
 	mainScript = 'main.nf'
-	version = '0.8.0'
+	version = '0.9.0'
 }
diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
index 355685bb..bdf85253 100644
--- a/configs/nextflow.hopper.config
+++ b/configs/nextflow.hopper.config
@@ -165,15 +165,15 @@ process {
 		publishDir = [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true, pattern: '*.cdmpy' ] ]
 	}
 	withName: create_analysis_result {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.10.0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
 	}
 	withName: create_cdm_input {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.10.0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.10.0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ]
 		ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
 		ext.args_sourmash = {"${params.outdir}/${params.speciesDir}/sourmash"}
@@ -223,7 +223,7 @@ process {
 	}
 	withName: post_align_qc {
 		memory = '2 GB'
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.10.0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
 	}
 	withName: quast {
@@ -246,7 +246,7 @@ process {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: save_analysis_metadata {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
+		container = "docker://clinicalgenomicslund/bonsai-prp:0.10.0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
 	withName: serotypefinder {
@@ -311,5 +311,5 @@ manifest {
 	homePage = 'https://github.com/genomic-medicine-sweden/jasen'
 	description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes'
 	mainScript = 'main.nf'
-	version = '0.8.0'
+	version = '0.9.0'
 }
diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
index 0434d6a3..a566cebf 100644
--- a/configs/nextflow.ngp.config
+++ b/configs/nextflow.ngp.config
@@ -321,5 +321,5 @@ manifest {
 	homePage = 'https://github.com/genomic-medicine-sweden/jasen'
 	description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes'
 	mainScript = 'main.nf'
-	version = '0.8.0'
+	version = '0.9.0'
 }