Merge pull request #75 from nf-core/dev

Release 2.0.2

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
   # Fake the tag locally so that the pipeline runs properly
-  - docker tag nfcore/eager nfcore/eager:2.0.1
+  - docker tag nfcore/eager nfcore/eager:2.0.2
 
 install:
   # Install Nextflow
@@ -22,6 +22,10 @@ install:
   - sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow
   # Install nf-core/tools
   - pip install nf-core
+  # Install Conda 
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
+  - bash Miniconda3-latest-Linux-x86_64.sh -b -f -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
   # Reset
   - mkdir ${TRAVIS_BUILD_DIR}/tests && cd ${TRAVIS_BUILD_DIR}/tests
 
@@ -44,3 +48,5 @@ script:
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --circularmapper --circulartarget 'NC_007596.2'
   # Test running with BWA Mem
   - nextflow run ${TRAVIS_BUILD_DIR} -profile test,docker --pairedEnd --bwamem
+  # Test basic pipeline with Conda too 
+  - nextflow run ${TRAVIS_BUILD_DIR} -profile test,conda --pairedEnd

CHANGELOG.md

@@ -4,9 +4,23 @@ 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+## unpublished
+
+
+## [2.0.2] - 2018-11-03
+
+### `Changed`
+* [#70](https://github.com/nf-core/eager/issues/70) - Uninitialized `readPaths` warning removed
+
+### `Added`
+* [#73](https://github.com/nf-core/eager/pull/73) - Travis CI Testing of Conda Environment added 
+
+### `Fixed`
+* [#72](https://github.com/nf-core/eager/issues/72) - iconv Issue with R in conda environment
+
 ## [2.0.1] - 2018-11-02
 
-### `Fixed`s
+### `Fixed`
 
 * [#69](https://github.com/nf-core/eager/issues/67) - FastQC issues with conda environments
 

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-2.0.1/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.0.2/bin:$PATH

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 2.0.1
+    VERSION 2.0.2
 
 %environment
-    PATH=/opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH
+    PATH=/opt/conda/envs/nf-core-eager-2.0.2/bin:$PATH
     export PATH
 
 %files

environment.yml

@@ -1,4 +1,4 @@
-name: nf-core-eager-2.0.1
+name: nf-core-eager-2.0.2
 channels:
   - defaults
   - bioconda
@@ -20,7 +20,8 @@ dependencies:
   - damageprofiler=0.3.11
   - multiqc=1.6
   - pmdtools=0.60
-  - r-markdown=0.8
+  - r-rmarkdown=1.10
+  - libiconv=1.15
   - sequencetools=1.2.2
   - preseq=2.0.3
   - fastp=0.19.4

nextflow.config

@@ -11,7 +11,7 @@
 // Global default params, used in configs
 params {
   pipelineVersion = '2.0.0dev' // Pipeline version
-  container = 'nfcore/eager:2.0.1'
+  container = 'nfcore/eager:2.0.2'
 
   //Pipeline options
   aligner = 'bwa'
@@ -22,6 +22,7 @@ params {
   reads = "data/*{1,2}.fastq.gz"
   outdir = './results'
   tracedir = "${params.outdir}/pipeline_info"
+  readPaths = false
 
   //More defaults
   complexity_filter = false
@@ -99,7 +100,7 @@ manifest {
   name = 'nf-core/eager'
   author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates'
   homePage = 'https://github.com/nf-core/eager'
-  version = '2.0.1'
+  version = '2.0.2'
   description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '>=0.32.0'