diff --git a/.travis.yml b/.travis.yml index aa0f453c0..2b056242c 100644 --- a/.travis.yml +++ b/.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 ${TRAVIS_BUILD_DIR} -profile test,conda --pairedEnd \ No newline at end of file diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d581c034..fc60f786c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,9 +4,23 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## unpublished + + +## [2.0.2] - 2018-11-03 + +### `Changed` +* [#70](https://github.com/nf-core/eager/issues/70) - Uninitialized `readPaths` warning removed + +### `Added` +* [#73](https://github.com/nf-core/eager/pull/73) - Travis CI Testing of Conda Environment added + +### `Fixed` +* [#72](https://github.com/nf-core/eager/issues/72) - iconv Issue with R in conda environment + ## [2.0.1] - 2018-11-02 -### `Fixed`s +### `Fixed` * [#69](https://github.com/nf-core/eager/issues/67) - FastQC issues with conda environments diff --git a/Dockerfile b/Dockerfile index 429307a4a..de193795c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,4 +3,4 @@ FROM nfcore/base LABEL description="Docker image containing all requirements for nf-core/eager pipeline" COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-eager-2.0.2/bin:$PATH diff --git a/Singularity b/Singularity index 9460cfc7c..7e1d297ef 100644 --- a/Singularity +++ b/Singularity @@ -4,10 +4,10 @@ Bootstrap:docker %labels MAINTAINER Alexander Peltzer DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline - VERSION 2.0.1 + VERSION 2.0.2 %environment - PATH=/opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH + PATH=/opt/conda/envs/nf-core-eager-2.0.2/bin:$PATH export PATH %files diff --git a/environment.yml b/environment.yml index 9e2df0bf1..c1cae9da9 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: nf-core-eager-2.0.1 +name: nf-core-eager-2.0.2 channels: - defaults - bioconda @@ -20,7 +20,8 @@ dependencies: - damageprofiler=0.3.11 - multiqc=1.6 - pmdtools=0.60 - - r-markdown=0.8 + - r-rmarkdown=1.10 + - libiconv=1.15 - sequencetools=1.2.2 - preseq=2.0.3 - fastp=0.19.4 diff --git a/nextflow.config b/nextflow.config index 09ba2fe4d..3d7e9e93c 100644 --- a/nextflow.config +++ b/nextflow.config @@ -11,7 +11,7 @@ // Global default params, used in configs params { pipelineVersion = '2.0.0dev' // Pipeline version - container = 'nfcore/eager:2.0.1' + container = 'nfcore/eager:2.0.2' //Pipeline options aligner = 'bwa' @@ -22,6 +22,7 @@ params { reads = "data/*{1,2}.fastq.gz" outdir = './results' tracedir = "${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'