Prepare release

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/sarek:dev
   # Fake the tag locally so that the pipeline runs properly
   # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/sarek:dev nfcore/sarek:dev
+  - docker tag nfcore/sarek:dev nfcore/sarek:2.5
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -5,7 +5,7 @@ All notable changes to this project will be documented in this file.
 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).
 
-## Unreleased
+## [2.5] - Ålkatj - 2019-09-XX
 
 Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.
 

Dockerfile

@@ -4,4 +4,4 @@ LABEL authors="Maxime Garcia" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-sarek-2.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-2.5/bin:$PATH

containers/snpeff/Dockerfile

@@ -7,7 +7,7 @@ LABEL \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-snpeff-2.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-snpeff-2.5/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38

containers/snpeff/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: sarek-snpeff-2.5dev
+name: sarek-snpeff-2.5
 channels:
   - conda-forge
   - bioconda

containers/vep/Dockerfile

@@ -7,7 +7,7 @@ LABEL \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-vep-2.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-vep-2.5/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38

containers/vep/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: sarek-vep-2.5dev
+name: sarek-vep-2.5
 channels:
   - conda-forge
   - bioconda

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-sarek-2.5dev
+name: nf-core-sarek-2.5
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -36,7 +36,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/sarek:dev'
+process.container = 'nfcore/sarek:2.5'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -105,7 +105,7 @@ manifest {
   description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.04.0'
-  version = '2.5dev'
+  version = '2.5'
 }
 
 // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over