From badd2a2a5c6727a798a978b75b322e9b917bab52 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 1 Jul 2020 23:10:19 +0100 Subject: [PATCH 1/2] Bump versions --- .github/workflows/ci.yml | 8 ++++---- CHANGELOG.md | 2 +- Dockerfile | 4 ++-- environment.yml | 2 +- nextflow.config | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 5cfe6711..6c65240b 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:dev + run: docker build --no-cache . -t nfcore/chipseq:1.2.0 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/chipseq:dev - docker tag nfcore/chipseq:dev nfcore/chipseq:dev + docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0 - 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:dev + run: docker build --no-cache . -t nfcore/chipseq:1.2.0 - name: Pull docker image if: ${{ !env.GIT_DIFF }} run: | docker pull nfcore/chipseq:dev - docker tag nfcore/chipseq:dev nfcore/chipseq:dev + docker tag nfcore/chipseq:dev nfcore/chipseq:1.2.0 - name: Install Nextflow run: | diff --git a/CHANGELOG.md b/CHANGELOG.md index ba14fd71..1df4c104 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). -## [1.2.0] - 2020-06-04 +## [1.2.0] - 2020-07-02 ### `Added` diff --git a/Dockerfile b/Dockerfile index 878a9efa..0628abe4 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-chipseq-1.1.1dev/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-chipseq-1.2.0/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-chipseq-1.1.1dev > nf-core-chipseq-1.1.1dev.yml +RUN conda env export --name nf-core-chipseq-1.2.0 > nf-core-chipseq-1.2.0.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 a042f4e7..11207722 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-1.1.1dev +name: nf-core-chipseq-1.2.0 channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 877008de..4e54affd 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:dev' +process.container = 'nfcore/chipseq:1.2.0' // 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 = '1.1.1dev' + version = '1.2.0' } // Function to ensure that resource requirements don't go beyond From 1a4ef1a31b802930815b31b6ef5b3b15956419d2 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Wed, 1 Jul 2020 23:31:51 +0100 Subject: [PATCH 2/2] Update CHANGELOG --- CHANGELOG.md | 49 ++++++++++++++++++++++++------------------------- 1 file changed, 24 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1df4c104..aafc386f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,13 +11,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. * [#153](https://github.com/nf-core/chipseq/issues/153) - Add plotHeatmap * [#159](https://github.com/nf-core/chipseq/issues/159) - expose bwa mem -T parameter * [nf-core/atacseq#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore! -* [nf-core/atacseq#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated * [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report * [nf-core/atacseq#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2 * [nf-core/atacseq#79](https://github.com/nf-core/atacseq/issues/79) - Parallelize DESeq2 * [nf-core/atacseq#97](https://github.com/nf-core/atacseq/issues/97) - PBC1, PBC2 from pipeline? * [nf-core/atacseq#107](https://github.com/nf-core/atacseq/issues/107) - Add options to change MACS2 parameters -* [nf-core/atacseq#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf? * Regenerated screenshots and added collapsible sections for output files in `docs/output.md` * Update template to tools `1.9` * Replace `set` with `tuple` and `file()` with `path()` in all processes @@ -34,53 +32,54 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ### `Removed` -* `--tss_bed` +* `--tss_bed` parameter ### `Fixed` * [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE * [#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system * [#154](https://github.com/nf-core/chipseq/issues/154) - computeMatrix.val.mat.gz files not zipped +* [nf-core/atacseq#71](https://github.com/nf-core/atacseq/issues/71) - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated * [nf-core/atacseq#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created * [nf-core/atacseq#86](https://github.com/nf-core/atacseq/issues/86) - bug in the plot_homer_annotatepeaks.r script * [nf-core/atacseq#102](https://github.com/nf-core/atacseq/issues/102) - Incorrect Group ID assigned by featurecounts_deseq2.r +* [nf-core/atacseq#109](https://github.com/nf-core/atacseq/issues/109) - Specify custom gtf but gene bed is not generated from that gtf? * Make executables in `bin/` compatible with Python 3 ### `Dependencies` -* Add python `3.7.6` +* Add bioconductor-biocparallel `1.20.0` * Add markdown `3.2.2` -* Add pymdown-extensions `7.1` -* Add pygments `2.6.1` * Add pigz `2.3.4` -* Add r-tidyr `1.1.0` +* Add pygments `2.6.1` +* Add pymdown-extensions `7.1` +* Add python `3.7.6` * Add r-reshape2 `1.4.4` -* Add bioconductor-biocparallel `1.20.0` +* Add r-tidyr `1.1.0` +* Update bedtools `2.27.1` -> `2.29.2` +* Update bioconductor-deseq2 `1.20.0` -> `1.26.0` +* Update bioconductor-vsn `3.46.0` -> `3.54.0` +* Update deeptools `3.2.1` -> `3.4.3` +* Update fastqc `0.11.8` -> `0.11.9` * Update gawk `4.2.1` -> `5.1.0` +* Update homer `4.9.1` -> `4.11` +* Update macs2 `2.1.2` -> `2.2.7.1` +* Update multiqc `1.7` -> `1.8` +* Update phantompeakqualtools `1.2` -> `1.2.2` +* Update picard `2.19.0` -> `2.23.1` +* Update pysam `0.15.2` -> `0.15.3` * Update r-base `3.4.1` -> `3.6.2` -* Update r-optparse `1.6.0` -> `1.6.6` * Update r-ggplot2 `3.1.0` -> `3.3.2` -* Update r-pheatmap `1.0.10` -> `1.0.12` * Update r-lattice `0.20_35` -> `0.20_41` -* Update r-upsetr `1.3.3` -> `1.4.0` +* Update r-optparse `1.6.0` -> `1.6.6` +* Update r-pheatmap `1.0.10` -> `1.0.12` * Update r-scales `1.0.0` -> `1.1.1` +* Update r-upsetr `1.3.3` -> `1.4.0` * Update r-xfun `0.3` -> `0.15` -* Update fastqc `0.11.8` -> `0.11.9` -* Update trim-galore `0.5.0` -> `0.6.5` * Update samtools `1.9` -> `1.10` -* Update picard `2.19.0` -> `2.23.1` -* Update pysam `0.15.2` -> `0.15.3` -* Update bedtools `2.27.1` -> `2.29.2` -* Update ucsc-bedgraphtobigwig `377` -> `357` -* Update deeptools `3.2.1` -> `3.4.3` -* Update macs2 `2.1.2` -> `2.2.7.1` -* Update homer `4.9.1` -> `4.11` * Update subread `1.6.4` -> `2.0.1` -* Update multiqc `1.7` -> `1.8` -* Update phantompeakqualtools `1.2` -> `1.2.2` -* Update bioconductor-deseq2 `1.20.0` -> `1.26.0` -* Update bioconductor-vsn `3.46.0` -> `3.54.0` -* Remove r-reshape2 `1.4.3` +* Update trim-galore `0.5.0` -> `0.6.5` +* Update ucsc-bedgraphtobigwig `377` -> `357` ## [1.1.0] - 2019-11-05