Merge pull request #660 from jfy133/dev

Patch release with readgroup fixes and to get docker working

Author: jfy133

.github/workflows/ci.yml

@@ -34,13 +34,13 @@ 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:2.3.1
 
       - 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:2.3.1
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,14 +3,15 @@
 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).
 
-## [2.3.1dev] - Unreleased
+## [2.3.1] - 2021-01-14
 
 ### `Added`
 
 ### `Fixed`
 
 - [#654](https://github.com/nf-core/eager/issues/654) - Fixed some values in JSON schema (used in launch GUI) not passing validation checks during run
 - [#655](https://github.com/nf-core/eager/issues/655) - Updated read groups for all mappers to allow proper GATK validation
+- Fixed issue with Docker container not being pullable by Nextflow due to version-number inconsistencies
 
 ### `Dependencies`
 

Dockerfile

@@ -7,10 +7,10 @@ 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-2.3.1dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.3.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.3.1dev > nf-core-eager-2.3.1dev.yml
+RUN conda env export --name nf-core-eager-2.3.1 > nf-core-eager-2.3.1.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

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-2.3.1dev
+name: nf-core-eager-2.3.1
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -251,7 +251,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:dev'
+process.container = 'nfcore/eager:2.3.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -345,7 +345,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.04.0'
-  version = '2.3.1dev'
+  version = '2.3.1'
 }
 
 // Function to ensure that resource requirements don't go beyond