diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bdf469a2..766da031 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/atacseq:1.2.1 + run: docker build --no-cache . -t nfcore/atacseq:1.2.2 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/atacseq:dev - docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.1 + docker tag nfcore/atacseq:dev nfcore/atacseq: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/atacseq:1.2.1 + run: docker build --no-cache . -t nfcore/atacseq:1.2.2 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/atacseq:dev - docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.1 + docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.2 - name: Install Nextflow run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index 9afecd1b..a458135d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,14 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## [1.2.2] - 2022-04-29 + +* Minor patch release to fix Conda environment and enable DSL1 by default in the `nextflow.config`. +### `Dependencies` + +* Update r-base `3.6.2` -> `3.6.3` +* Update r-xfun `0.15` -> `0.22` + ## [1.2.1] - 2020-07-29 * [#118](https://github.com/nf-core/atacseq/issues/118) - Minor patch release to update pipeline schema diff --git a/Dockerfile b/Dockerfile index bb346cc3..dac76775 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-atacseq-1.2.1/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-atacseq-1.2.2/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-atacseq-1.2.1 > nf-core-atacseq-1.2.1.yml +RUN conda env export --name nf-core-atacseq-1.2.2 > nf-core-atacseq-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/environment.yml b/environment.yml index 2d88b67f..acf02a8e 100755 --- 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-atacseq-1.2.1 +name: nf-core-atacseq-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=0.22 - conda-forge::gawk=5.1.0 - conda-forge::pigz=2.3.4 ## Required for TrimGalore multi-threading diff --git a/nextflow.config b/nextflow.config index 29bdf0df..702c9b53 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,6 +5,10 @@ * Default config options for all environments. */ +// From nextflow version 22.04.0, DSL1 becomes the default mode +// see here: https://www.nextflow.io/blog/2022/evolution-of-nextflow-runtime.html +nextflow.enable.dsl = 1 + // Global default params, used in configs params { @@ -99,7 +103,7 @@ params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev -process.container = 'nfcore/atacseq:1.2.1' +process.container = 'nfcore/atacseq:1.2.2' // Load base.config by default for all pipelines includeConfig 'conf/base.config'