Merge pull request #222 from apeltzer/dev

Bumped to 2.0.7

Author: apeltzer

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/eager: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/eager:dev nfcore/eager:dev
+  - docker tag nfcore/eager:dev nfcore/eager:2.0.7
 
 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).
 
-## [Unpublished Version / DEV]
+## [2.0.7] - 2019-06-10
 
 ### `Added`
 
@@ -17,7 +17,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 * Don't ignore DamageProfiler errors anymore 
 * [#220](https://github.com/nf-core/eager/pull/220) - Added post-mapping filtering statistics module and corresponding MultiQC statistics [#217](https://github.com/nf-core/eager/issues/217)
 
-
 ### `Fixed`
 
 * [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
@@ -34,10 +33,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 * Added DeDup v0.12.5 (json support)
 * Added mtnucratio v0.5 (json support)
-* Updated Picard 2.18.27 -> 2.19.0
-* Updated GATK 4.1.0.0 -> 4.1.1.1
-* Updated damageprofiler 0.4.4 -> 0.4.5 
+* Updated Picard 2.18.27 -> 2.20.2
+* Updated GATK 4.1.0.0 -> 4.1.2.0
+* Updated damageprofiler 0.4.4 -> 0.4.5
 * Updated r-rmarkdown 1.11 -> 1.12
+* Updated fastp 0.19.7 -> 0.20.0
+* Updated qualimap 2.2.2b -> 2.2.2c
 
 ## [2.0.6] - 2019-03-05
 

Dockerfile

@@ -3,4 +3,4 @@ FROM nfcore/base
 LABEL description="Docker image containing all requirements for nf-core/eager pipeline"
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-eager-2.0.7dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.7/bin:$PATH

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.7dev
+name: nf-core-eager-2.0.7
 channels:
   - defaults
   - bioconda
@@ -9,13 +9,13 @@ dependencies:
   - bioconda::adapterremoval=2.2.2
   - bioconda::adapterremovalfixprefix=0.0.4
   - bioconda::bwa=0.7.17
-  - bioconda::picard=2.19.0
+  - bioconda::picard=2.20.2
   - bioconda::samtools=1.9
   - bioconda::dedup=0.12.5
   - bioconda::angsd=0.923
   - bioconda::circularmapper=1.93.4
-  - bioconda::gatk4=4.1.1.0
-  - bioconda::qualimap=2.2.2b
+  - bioconda::gatk4=4.1.2.0
+  - bioconda::qualimap=2.2.2c
   - bioconda::vcf2genome=0.91
   - bioconda::damageprofiler=0.4.6
   - bioconda::multiqc=1.7
@@ -25,7 +25,7 @@ dependencies:
   - conda-forge::pigz=2.3.4
   - bioconda::sequencetools=1.2.2
   - bioconda::preseq=2.0.3
-  - bioconda::fastp=0.19.7
+  - bioconda::fastp=0.20.0
   - bioconda::bamutil=1.0.14
   - bioconda::mtnucratio=0.5
   - pysam=0.15.2

nextflow.config

@@ -50,7 +50,7 @@ params {
 }
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:dev'
+process.container = 'nfcore/eager:2.0.7'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -104,7 +104,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A. Fellows Yates, Maxime Borry'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.7dev'
+  version = '2.0.7'
   description = 'A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'