Merge pull request #69 from nf-core/dev

PR for release 2.0.1

.travis.yml

@@ -13,7 +13,7 @@ before_install:
   # Pull the docker image first so the test doesn't wait for this
   - docker pull nfcore/eager
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/eager nfcore/eager:2.0.0
+  - docker tag nfcore/eager nfcore/eager:2.0.1
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -1,8 +1,20 @@
 # nf-core/eager: Changelog
+All notable changes to this project will be documented in this file.
 
-## 2.0 "Kaufbeuren" - 2018-10-17
+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).
 
-Initial release of nf-core/eager featuring:
+## [2.0.1] - 2018-11-02
+
+### `Fixed`s
+
+* [#69](https://github.com/nf-core/eager/issues/67) - FastQC issues with conda environments
+
+## [2.0.0] "Kaufbeuren" - 2018-10-17
+
+Initial release of nf-core/eager:
+
+### `Added`
 
 * FastQC read quality control
 * (Optional) Read complexity filtering with FastP

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-2.0.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH

README.md

@@ -6,6 +6,9 @@
 [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/)
 [![Docker Container available](https://img.shields.io/docker/automated/nfcore/eager.svg)](https://hub.docker.com/r/nfcore/eager/)
 ![Singularity Container available](https://img.shields.io/badge/singularity-available-7E4C74.svg)
+[![DOI](https://zenodo.org/badge/135918251.svg)](https://zenodo.org/badge/latestdoi/135918251)
+
+
 
 ## Introduction
 

Singularity

@@ -4,10 +4,10 @@ Bootstrap:docker
 %labels
     MAINTAINER Alexander Peltzer <[email protected]>
     DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline
-    VERSION 2.0.0
+    VERSION 2.0.1
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.0/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH
     export PATH
 
 %files

environment.yml

@@ -1,18 +1,18 @@
-name: nf-core-eager-2.0.0
+name: nf-core-eager-2.0.1
 channels:
   - defaults
-  - conda-forge
   - bioconda
+  - conda-forge
 dependencies:
-  - conda-forge::openjdk=8.0.144 # Needed for FastQC docker - see bioconda/bioconda-recipes#5026
+  - defaults::openjdk=8.0.152
   - fastqc=0.11.8
   - adapterremoval=2.2.2
   - adapterremovalfixprefix=0.0.4
   - bwa=0.7.17
-  - picard=2.18.14
+  - picard=2.18.15
   - samtools=1.9
   - dedup=0.12.3
-  - angsd=0.921
+  - angsd=0.923
   - circularmapper=1.93.4
   - gatk4=4.0.10.0
   - qualimap=2.2.2b

nextflow.config

@@ -11,7 +11,7 @@
 // Global default params, used in configs
 params {
   pipelineVersion = '2.0.0dev' // Pipeline version
-  container = 'nfcore/eager:2.0.0'
+  container = 'nfcore/eager:2.0.1'
 
   //Pipeline options
   aligner = 'bwa'
@@ -41,7 +41,6 @@ profiles {
   }
   singularity {
     singularity.enabled = true
-    process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"}
   }
   standard {
     includeConfig 'conf/base.config'
@@ -100,7 +99,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.0'
+  version = '2.0.1'
   description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'