Merge pull request #620 from jfy133/dev

Version bump for patch release

.github/workflows/awsfulltest.yml

@@ -23,7 +23,6 @@ jobs:
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command

.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:2.2.2
 
       - 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:2.2.2
 
       - name: Install Nextflow
         env:

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).
 
-## [2.2.2dev] - Unreleased
+## [2.2.2] - 2020-12-03
 
 ### `Added`
 
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#602](https://github.com/nf-core/eager/issues/602) - Added the newly avaliable GATK 3.5 conda package.
 - [#610](https://github.com/nf-core/eager/issues/610) - Create bwa_index channel when specifying circularmapper as mapper
 - Updated template to nf-core/tools 1.12
+- General documentation improvements
 
 ### `Deprecated`
 

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-2.2.2dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.2.2/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.2.2dev > nf-core-eager-2.2.2dev.yml
+RUN conda env export --name nf-core-eager-2.2.2 > nf-core-eager-2.2.2.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

bin/scrape_software_versions.py

@@ -3,7 +3,6 @@
 from collections import OrderedDict
 import re
 
-# TODO nf-core: Add additional regexes for new tools in process get_software_versions
 regexes = {
     "nf-core/eager": ["v_pipeline.txt", r"(\S+)"],
     "Nextflow": ["v_nextflow.txt", r"(\S+)"],

environment.yml

@@ -1,15 +1,15 @@
-name: nf-core-eager-2.2.2dev
+name: nf-core-eager-2.2.2
 channels:
   - conda-forge
   - bioconda
   - defaults
 dependencies:
   - conda-forge::python=3.7.3
-  - conda-forge::markdown=3.2.2 #Dont upgrade anymore
+  - conda-forge::markdown=3.2.2 #Don't upgrade anymore
   - conda-forge::pymdown-extensions=7.1
   - conda-forge::pygments=2.6.1
   - bioconda::rename=1.601
-  - conda-forge::openjdk=8.0.144
+  - conda-forge::openjdk=8.0.144 # Don't upgrade - required for GATK
   - bioconda::fastqc=0.11.9
   - bioconda::adapterremoval=2.3.1
   - bioconda::adapterremovalfixprefix=0.0.5
@@ -20,10 +20,10 @@ dependencies:
   - bioconda::angsd=0.933
   - bioconda::circularmapper=1.93.5
   - bioconda::gatk4=4.1.7.0
-  - bioconda::gatk=3.5
+  - bioconda::gatk=3.5 ## Don't upgrade - required for MultiVCFAnalyzer
   - bioconda::qualimap=2.2.2d
   - bioconda::vcf2genome=0.91
-  - bioconda::damageprofiler=0.4.9
+  - bioconda::damageprofiler=0.4.9 # Don't upgrade - later versions don't allow java 8
   - bioconda::multiqc=1.9
   - bioconda::pmdtools=0.60
   - bioconda::bedtools=2.29.2

nextflow.config

@@ -243,7 +243,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:dev'
+process.container = 'nfcore/eager:2.2.2'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -337,7 +337,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.04.0'
-  version = '2.2.2dev'
+  version = '2.2.2'
 }
 
 // Function to ensure that resource requirements don't go beyond