Bump versions for release

Author: jfy133

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:dev
+        run: docker build --no-cache . -t nfcore/eager:2.4.0
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:dev
+          docker tag nfcore/eager:dev nfcore/eager:2.4.0
 
       - name: Install Nextflow
         env:
@@ -212,4 +212,4 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: RESCALING Run basic pipeline with basic pipeline but with mapDamage rescaling of BAM files. Note this will be slow
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## v2.4dev - [unreleased]
+## [2.4.0] - 20201-08-31
 
 ### `Added`
 
@@ -51,7 +51,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Deprecated`
 
-## v2.3.5 - 2021-06-03
+## [2.3.5] - 2021-06-03
 
 ### `Added`
 
@@ -75,7 +75,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Deprecated`
 
-## v2.3.4 - 2021-05-05
+## [2.3.4] - 2021-05-05
 
 ### `Added`
 
@@ -96,7 +96,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Deprecated`
 
-## v2.3.3 - 2021-04-08
+## [2.3.3] - 2021-04-08
 
 ### `Added`
 

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.4dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.0/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4dev > nf-core-eager-2.4dev.yml
+RUN conda env export --name nf-core-eager-2.4.0 > nf-core-eager-2.4.0.yml

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-eager-2.4dev
+name: nf-core-eager-2.4.0
 channels:
   - conda-forge
   - bioconda
@@ -49,4 +49,4 @@ dependencies:
   - bioconda::eigenstratdatabasetools=1.0.2
   - bioconda::mapdamage2=2.2.1
   - bioconda::bbmap=38.92
-  - bioconda::bcftools=1.12
+  - bioconda::bcftools=1.12

nextflow.config

@@ -278,7 +278,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:dev'
+process.container = 'nfcore/eager:2.4.0'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -408,7 +408,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.4dev'
+  version = '2.4.0'
 }
 
 // Function to ensure that resource requirements don't go beyond