From e8f9e653e866a58cbae47c4f4240b20cbf1d9efb Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 22 Apr 2021 13:41:17 +0100 Subject: [PATCH 1/3] Update packages in environment --- environment.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/environment.yml b/environment.yml index 67a21782d..763fe309f 100644 --- a/environment.yml +++ b/environment.yml @@ -1,6 +1,6 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml -name: nf-core-chipseq-1.2.1 +name: nf-core-chipseq-1.2.2 channels: - conda-forge - bioconda @@ -11,7 +11,7 @@ dependencies: - conda-forge::markdown=3.2.2 - conda-forge::pymdown-extensions=7.1 - conda-forge::pygments=2.6.1 - - conda-forge::r-base=3.6.2 + - conda-forge::r-base=3.6.3 - conda-forge::r-optparse=1.6.6 - conda-forge::r-rcolorbrewer=1.1_2 - conda-forge::r-reshape2=1.4.4 @@ -21,7 +21,7 @@ dependencies: - conda-forge::r-pheatmap=1.0.12 - conda-forge::r-lattice=0.20_41 - conda-forge::r-upsetr=1.4.0 - - conda-forge::r-xfun=0.15 + - conda-forge::r-xfun=0.20 - conda-forge::gawk=5.1.0 - conda-forge::pigz=2.3.4 ## Required for TrimGalore multi-threading From f13b5d6f885b64df0edc857f9369cdc43ebb9d18 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 22 Apr 2021 13:41:49 +0100 Subject: [PATCH 2/3] Bump pipeline version from 1.2.1 -> 1.2.2 --- .github/workflows/ci.yml | 8 ++++---- CHANGELOG.md | 4 ++++ Dockerfile | 4 ++-- nextflow.config | 4 ++-- 4 files changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5740990aa..e00789bce 100755 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -35,13 +35,13 @@ jobs: - name: Build new docker image if: env.GIT_DIFF - run: docker build --no-cache . -t nfcore/chipseq:1.2.1 + run: docker build --no-cache . -t nfcore/chipseq:1.2.2 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/chipseq:dev - docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.1 + docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.2 - name: Install Nextflow run: | @@ -75,13 +75,13 @@ jobs: - name: Build new docker image if: env.GIT_DIFF - run: docker build --no-cache . -t nfcore/chipseq:1.2.1 + run: docker build --no-cache . -t nfcore/chipseq:1.2.2 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/chipseq:dev - docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.1 + docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.2 - name: Install Nextflow run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index fc587ef09..b83e56e9f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [1.2.2] - 2021-04-22 + +* [#206](https://github.com/nf-core/chipseq/issues/206) - Minor patch release to fix Conda environment + ## [1.2.1] - 2020-07-29 * [#171](https://github.com/nf-core/chipseq/issues/171) - Minor patch release to update pipeline schema diff --git a/Dockerfile b/Dockerfile index 44ec4adfa..13ec872b4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.1/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.2/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-chipseq-1.2.1 > nf-core-chipseq-1.2.1.yml +RUN conda env export --name nf-core-chipseq-1.2.2 > nf-core-chipseq-1.2.2.yml # Instruct R processes to use these empty files instead of clashing with a local version RUN touch .Rprofile diff --git a/nextflow.config b/nextflow.config index 561fe9d7a..71f62859d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -96,7 +96,7 @@ params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev -process.container = 'nfcore/chipseq:1.2.1' +process.container = 'nfcore/chipseq:1.2.2' // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -169,7 +169,7 @@ manifest { description = 'ChIP-seq peak-calling and differential analysis pipeline.' mainScript = 'main.nf' nextflowVersion = '>=19.10.0' - version = '1.2.1' + version = '1.2.2' } // Function to ensure that resource requirements don't go beyond From 801bc537dbe006d881df60b4b50a4e1c91352c90 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 22 Apr 2021 16:22:18 +0100 Subject: [PATCH 3/3] Update CHANGELOG.md --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index b83e56e9f..1a66ef72c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * [#206](https://github.com/nf-core/chipseq/issues/206) - Minor patch release to fix Conda environment +### `Dependencies` + +* Update r-base `3.6.2` -> `3.6.3` +* Update r-xfun `0.15` -> `0.20` + ## [1.2.1] - 2020-07-29 * [#171](https://github.com/nf-core/chipseq/issues/171) - Minor patch release to update pipeline schema