From 3f547e407177b6978e2810738913892e7c95f7a6 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 2 Nov 2018 14:53:57 +0100 Subject: [PATCH 1/6] Fix typo --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7d581c034..746fdd8bf 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,7 +6,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ## [2.0.1] - 2018-11-02 -### `Fixed`s +### `Fixed` * [#69](https://github.com/nf-core/eager/issues/67) - FastQC issues with conda environments From 33e05470e9011b40a3b64e69cc363f5b32c65b71 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 2 Nov 2018 14:59:40 +0100 Subject: [PATCH 2/6] Bumping to 2.0.2 --- .travis.yml | 8 +++++++- Dockerfile | 2 +- Singularity | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 5 files changed, 13 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index aa0f453c0..3b29c207b 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:latest 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 ${TRAVIS_BUILD_DIR} -profile test,conda --pairedEnd \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index 429307a4a..e846ab671 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,4 +3,4 @@ FROM nfcore/base LABEL description="Docker image containing all requirements for nf-core/eager pipeline" COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-eager-2.0.2dev/bin:$PATH diff --git a/Singularity b/Singularity index 9460cfc7c..ef5885b7b 100644 --- a/Singularity +++ b/Singularity @@ -4,10 +4,10 @@ Bootstrap:docker %labels MAINTAINER Alexander Peltzer DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline - VERSION 2.0.1 + VERSION 2.0.2dev %environment - PATH=/opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH + PATH=/opt/conda/envs/nf-core-eager-2.0.2dev/bin:$PATH export PATH %files diff --git a/environment.yml b/environment.yml index 9e2df0bf1..60f3dd061 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: nf-core-eager-2.0.1 +name: nf-core-eager-2.0.2dev channels: - defaults - bioconda diff --git a/nextflow.config b/nextflow.config index 09ba2fe4d..8f9898d5b 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:latest' //Pipeline options aligner = 'bwa' @@ -99,7 +99,7 @@ manifest { name = 'nf-core/eager' author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates' homePage = 'https://github.com/nf-core/eager' - version = '2.0.1' + version = '2.0.2dev' description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.' mainScript = 'main.nf' nextflowVersion = '>=0.32.0' From 4b2491d4409f83a9d1e53b619fa7875fa1ca32c2 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 2 Nov 2018 15:07:44 +0100 Subject: [PATCH 3/6] Changelog updates for 2.0.2 --- CHANGELOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 746fdd8bf..3b735f327 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,14 @@ 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). +## [2.0.2dev] + +### `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 + ## [2.0.1] - 2018-11-02 ### `Fixed` From 9c287ae8055856248adbbc3dd88eab70fc5cac41 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 2 Nov 2018 15:10:06 +0100 Subject: [PATCH 4/6] Initialize readPaths --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index 8f9898d5b..20260a4ed 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 From 1e9075b6a53275593fc112254e5cd120cfc66e41 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sat, 3 Nov 2018 14:47:59 +0100 Subject: [PATCH 5/6] Should fix libiconv issues --- environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 60f3dd061..09d02c231 100644 --- a/environment.yml +++ b/environment.yml @@ -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 From a657d09572dfed0868af4e26a09711e84fa0ef52 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Sat, 3 Nov 2018 16:22:45 +0100 Subject: [PATCH 6/6] Fixing iconv issues #72 --- .travis.yml | 2 +- CHANGELOG.md | 8 +++++++- Dockerfile | 2 +- Singularity | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 6 files changed, 14 insertions(+), 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index 3b29c207b..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:latest + - docker tag nfcore/eager nfcore/eager:2.0.2 install: # Install Nextflow diff --git a/CHANGELOG.md b/CHANGELOG.md index 3b735f327..fc60f786c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,10 @@ 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). -## [2.0.2dev] +## unpublished + + +## [2.0.2] - 2018-11-03 ### `Changed` * [#70](https://github.com/nf-core/eager/issues/70) - Uninitialized `readPaths` warning removed @@ -12,6 +15,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `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` diff --git a/Dockerfile b/Dockerfile index e846ab671..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-2.0.2dev/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-eager-2.0.2/bin:$PATH diff --git a/Singularity b/Singularity index ef5885b7b..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 2.0.2dev + VERSION 2.0.2 %environment - PATH=/opt/conda/envs/nf-core-eager-2.0.2dev/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 09d02c231..c1cae9da9 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: nf-core-eager-2.0.2dev +name: nf-core-eager-2.0.2 channels: - defaults - bioconda diff --git a/nextflow.config b/nextflow.config index 20260a4ed..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:latest' + container = 'nfcore/eager:2.0.2' //Pipeline options aligner = 'bwa' @@ -100,7 +100,7 @@ manifest { name = 'nf-core/eager' author = 'Alexander Peltzer, Stephen Clayton, James A Fellows-Yates' homePage = 'https://github.com/nf-core/eager' - version = '2.0.2dev' + 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'