From 1b24f13b79a05242b30aec5d1a9981fdee1e30c8 Mon Sep 17 00:00:00 2001
From: LysianeBouchard <lysiane.bouchard.hsj@ssss.gouv.qc.ca>
Date: Thu, 5 Dec 2024 11:10:12 -0500
Subject: [PATCH] feat: CLIN-3614 bump version to 2.3.0-dev

---
 CHANGELOG.md        | 4 +++-
 README.md           | 2 +-
 conf/modules.config | 2 +-
 docs/usage.md       | 2 +-
 nextflow.config     | 2 +-
 5 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9913321..da46d0c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,8 +3,10 @@
 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).
 
+## v2.3.0-dev - [date]
 
-## v2.2.0-dev - [date]
+
+## v2.2.0-dev
 
 ### `Added`
 - [#41](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/41) Allow to customize the vep command
diff --git a/README.md b/README.md
index ed0007c..0f2ce45 100644
--- a/README.md
+++ b/README.md
@@ -38,7 +38,7 @@ This schema was done using [inkscape](https://inkscape.org/) with the good prati
 Here is an example nextflow command to run the pipeline:
 
 ```bash
-nextflow run -c cluster.config Ferlab-Ste-Justine/Post-processing-Pipeline -r "v2.2.0" \
+nextflow run -c cluster.config Ferlab-Ste-Justine/Post-processing-Pipeline -r "v2.3.0" \
     -params-file params.json  \
    --input samplesheet.csv \
    --outdir results/dir \
diff --git a/conf/modules.config b/conf/modules.config
index 3c048ac..b13ff28 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -49,7 +49,7 @@ process {
     }
 
     withName: EXOMISER { 
-        container = 'ferlabcrsj/exomiser:2.0.0'
+        container = 'ferlabcrsj/exomiser:2.3.0'
         publishDir = [
             path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
diff --git a/docs/usage.md b/docs/usage.md
index c9db878..915a793 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -54,7 +54,7 @@ These files must be correctly downloaded and specified through pipeline paramete
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run -c cluster.config Ferlab-Ste-Justine/Post-processing-Pipeline -r "v2.2.0" \
+nextflow run -c cluster.config Ferlab-Ste-Justine/Post-processing-Pipeline -r "v2.3.0" \
     -params-file params.json  \
    --input samplesheet.csv \
    --outdir results/dir \
diff --git a/nextflow.config b/nextflow.config
index 788524a..7375d05 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -369,7 +369,7 @@ manifest {
     description     = """Variant analysis for genome and exome GVCFs"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.10.1'
-    version         = '2.2.0-dev'
+    version         = '2.3.0-dev'
     doi             = ''
 }