Merge pull request #119 from apeltzer/dev

PR Bump for 2.0.4

Author: apeltzer

.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:dev
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/eager:dev nfcore/eager:latest
+  - docker tag nfcore/eager:dev nfcore/eager:2.0.4
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -6,11 +6,14 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## [Unpublished / Dev Branch]
 
+## [2.0.4] - 2019-01-07
+
 ### `Added`
 * [#111](https://github.com/nf-core/eager/pull/110) - Allow [Zipped FastA reference input](https://github.com/nf-core/eager/issues/91)
-* [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow. 
+* [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow 
 * [#114](https://github.com/nf-core/eager/pull/113) - Add proper runtime defaults for multiple processes 
-* [#118](https://github.com/nf-core/eager/pull/118) - Add centralized configs handling
+* [#118](https://github.com/nf-core/eager/pull/118) - Add centralized configs handling by https://github.com/nf-core/configs
+* [#115](https://github.com/nf-core/eager/pull/115) - Add DamageProfiler MultiQC support
 
 ### `Fixed`
 * [#110](https://github.com/nf-core/eager/pull/110) - Fix for [MultiQC Missing Second FastQC report](https://github.com/nf-core/eager/issues/107)

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-2.0.4dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.4/bin:$PATH

Singularity

@@ -4,10 +4,10 @@ Bootstrap:docker
 %labels
     MAINTAINER Alexander Peltzer <alexander.peltzer@qbic.uni-tuebingen.de>
     DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline
-    VERSION 2.0.4dev
+    VERSION 2.0.4
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.4dev/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.4/bin:$PATH
     export PATH
 
 %files

conf/test.config

@@ -14,8 +14,7 @@ params {
   genome = "Custom"
   //Input data
   singleEnd = false
-  readPaths = [
-   ['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
+  readPaths = [['JK2782_TGGCCGATCAACGA_L008', ['https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R1_001.fastq.gz.tengrand.fq.gz','https://github.com/nf-core/test-datasets/raw/eager2/testdata/Mammoth/JK2782_TGGCCGATCAACGA_L008_R2_001.fastq.gz.tengrand.fq.gz']],
   ]
   // Genome references
   fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager2/reference/Mammoth_MT_Krause.fasta'

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.4dev
+name: nf-core-eager-2.0.4
 channels:
   - defaults
   - bioconda

nextflow.config

@@ -10,7 +10,7 @@
 
 // Global default params, used in configs
 params {
-  container = 'nfcore/eager:latest'
+  container = 'nfcore/eager:2.0.4'
 
   //Pipeline options
   aligner = 'bwa'
@@ -86,7 +86,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.4dev'
+  version = '2.0.4'
   description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'