From 9d867f988e5dae8276de01ab2ea70c8302a7e45f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 17 Oct 2018 23:23:28 +0200 Subject: [PATCH 1/7] Dev Branch to 2.1.0dev, DOI added --- .travis.yml | 2 +- Dockerfile | 2 +- README.md | 3 +++ Singularity | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 6 files changed, 10 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index 7b5cce20d..8d16d3178 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:2.0.0 + - docker tag nfcore/eager nfcore/eager:latest install: # Install Nextflow diff --git a/Dockerfile b/Dockerfile index cffd879a6..e370de2a6 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-2.0.0/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-eager-2.1.0dev/bin:$PATH diff --git a/README.md b/README.md index eed6776f7..1b1247d07 100644 --- a/README.md +++ b/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 diff --git a/Singularity b/Singularity index a2da2cb7d..64417b733 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 2.0.0 + VERSION 2.1.0dev %environment - PATH=/opt/conda/envs/nf-core-eager-2.0.0/bin:$PATH + PATH=/opt/conda/envs/nf-core-eager-2.1.0dev/bin:$PATH export PATH %files diff --git a/environment.yml b/environment.yml index ad22d3990..ac7dce26d 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: nf-core-eager-2.0.0 +name: nf-core-eager-2.1.0dev channels: - defaults - conda-forge diff --git a/nextflow.config b/nextflow.config index 928e1a34f..924e3f655 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:2.0.0' + container = 'nfcore/eager:latest' //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 = '2.0.0' + version = '2.1.0dev' description = 'A fully reproducible and modern ancient DNA pipeline in Nextflow and with cloud support.' mainScript = 'main.nf' nextflowVersion = '>=0.32.0' From c39cc07a4318154cff1075382c2b15e5ae9c0c36 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 24 Oct 2018 09:49:00 +0200 Subject: [PATCH 2/7] Fix channel orders --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index ac7dce26d..1abd5285d 100644 --- a/environment.yml +++ b/environment.yml @@ -1,8 +1,8 @@ name: nf-core-eager-2.1.0dev channels: - defaults - - conda-forge - bioconda + - conda-forge dependencies: - conda-forge::openjdk=8.0.144 # Needed for FastQC docker - see bioconda/bioconda-recipes#5026 - fastqc=0.11.8 From 4ac6d7a3300113e9fa1779e0225f23fdaf6ddf1a Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 31 Oct 2018 09:29:35 +0100 Subject: [PATCH 3/7] Fixing #67 with FastQC and JDK incompatibilities --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 1abd5285d..ebe9443dd 100644 --- a/environment.yml +++ b/environment.yml @@ -4,7 +4,7 @@ channels: - 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 From 44a41e7d2e47745eecb83122e888bb785ca5901f Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 31 Oct 2018 09:56:47 +0100 Subject: [PATCH 4/7] Minor bump for updated recipes --- environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/environment.yml b/environment.yml index ebe9443dd..d47bf2c17 100644 --- a/environment.yml +++ b/environment.yml @@ -9,10 +9,10 @@ dependencies: - 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 From dea05ed97b87b9319cf4ca9ba44ccaaae853ffd3 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Wed, 31 Oct 2018 10:58:45 +0100 Subject: [PATCH 5/7] Remove singularity hub usage, this is not reproducible --- nextflow.config | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 924e3f655..4a4cac30d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -41,7 +41,6 @@ profiles { } singularity { singularity.enabled = true - process.container = {"shub://${params.container.replace('nfcore', 'nf-core')}"} } standard { includeConfig 'conf/base.config' From ef63b542cfefd03373263296519b780af6216155 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 2 Nov 2018 14:10:50 +0100 Subject: [PATCH 6/7] PR for 2.0.1 fixing fastqc issues in conda --- .travis.yml | 2 +- Dockerfile | 2 +- Singularity | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.travis.yml b/.travis.yml index 8d16d3178..aa0f453c0 100644 --- a/.travis.yml +++ b/.travis.yml @@ -13,7 +13,7 @@ before_install: # Pull the docker image first so the test doesn't wait for this - docker pull nfcore/eager # Fake the tag locally so that the pipeline runs properly - - docker tag nfcore/eager nfcore/eager:latest + - docker tag nfcore/eager nfcore/eager:2.0.1 install: # Install Nextflow diff --git a/Dockerfile b/Dockerfile index e370de2a6..429307a4a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,4 +3,4 @@ FROM nfcore/base LABEL description="Docker image containing all requirements for nf-core/eager pipeline" COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/nf-core-eager-2.1.0dev/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH diff --git a/Singularity b/Singularity index 64417b733..9460cfc7c 100644 --- a/Singularity +++ b/Singularity @@ -4,10 +4,10 @@ Bootstrap:docker %labels MAINTAINER Alexander Peltzer DESCRIPTION Container image containing all requirements for the nf-core/eager pipeline - VERSION 2.1.0dev + VERSION 2.0.1 %environment - PATH=/opt/conda/envs/nf-core-eager-2.1.0dev/bin:$PATH + PATH=/opt/conda/envs/nf-core-eager-2.0.1/bin:$PATH export PATH %files diff --git a/environment.yml b/environment.yml index d47bf2c17..9e2df0bf1 100644 --- a/environment.yml +++ b/environment.yml @@ -1,4 +1,4 @@ -name: nf-core-eager-2.1.0dev +name: nf-core-eager-2.0.1 channels: - defaults - bioconda diff --git a/nextflow.config b/nextflow.config index 4a4cac30d..09ba2fe4d 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:2.0.1' //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 = '2.1.0dev' + 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' From 3778a787393393586e86d9299bd0959d00f952e0 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Fri, 2 Nov 2018 14:18:49 +0100 Subject: [PATCH 7/7] Add proper Changelog [skip_ci] --- CHANGELOG.md | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index dbee1c282..7d581c034 100644 --- a/CHANGELOG.md +++ b/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