From 0b1409ff1e4e1ac60ad5e2aed9c8a38d61aeb8da Mon Sep 17 00:00:00 2001 From: WackerO Date: Fri, 13 Dec 2024 12:46:53 +0100 Subject: [PATCH] Bump versions --- .github/workflows/ci.yml | 8 ++++---- CHANGELOG.md | 6 +++++- Dockerfile | 6 +++--- environment.yml | 2 +- modules/local/report.nf | 2 +- nextflow.config | 2 +- 6 files changed, 15 insertions(+), 11 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ddc61109..d1c4fb42 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -39,14 +39,14 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.4 + run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.5 # Change the version above and the third version below before/after release - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull ghcr.io/qbic-pipelines/rnadeseq:dev - docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.4 + docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.5 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 @@ -93,14 +93,14 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.4 + run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.5 # Change the version above and the third version below before/after release - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull ghcr.io/qbic-pipelines/rnadeseq:dev - docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.4 + docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.5 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 diff --git a/CHANGELOG.md b/CHANGELOG.md index 14d87c82..1eeca23f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## dev +## 2.5 - The Potato Eaters ### Added @@ -14,8 +14,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed +- [#260](https://github.com/qbic-pipelines/rnadeseq/pull/260) Release 2.5 +- [#259](https://github.com/qbic-pipelines/rnadeseq/pull/259) Bump versions for release 2.5 + ### Fixed +- [#258](https://github.com/qbic-pipelines/rnadeseq/pull/258) Fixed some comments for release (removed excess checks for pathway_adj_pval_threshold, added default explanation of that param to Execute_report.R, fixed some whitespace) - [#252](https://github.com/qbic-pipelines/rnadeseq/pull/252) Fixed github CI bug by updating actions/upload-artifact - [#250](https://github.com/qbic-pipelines/rnadeseq/pull/250) Fixed incorrect reading and indexing of contrast_pairs diff --git a/Dockerfile b/Dockerfile index e1a58e5c..25f490cf 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,14 +5,14 @@ LABEL org.opencontainers.image.authors="Gisela Gabernet, Alexander Peltzer, Oska LABEL org.opencontainers.image.licenses=MIT COPY environment.yml / #RUN conda install -c conda-forge mamba -RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.4 && \ +RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.5 && \ mamba clean --all --yes RUN apt-get update -qq && \ apt-get install -y zip procps ghostscript # Add conda installation dir to PATH -ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-2.4/bin:$PATH +ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-2.5/bin:$PATH # Dump the details of the installed packates to a file for posterity -RUN mamba env export --name qbic-pipelines-rnadeseq-2.4 > qbic-pipelines-rnadeseq-2.4.yml +RUN mamba env export --name qbic-pipelines-rnadeseq-2.5 > qbic-pipelines-rnadeseq-2.5.yml # Instruct R processes to use these empty files instead of clashing with a local config RUN touch .Rprofile RUN touch .Renviron diff --git a/environment.yml b/environment.yml index e3e8f268..45eccb99 100644 --- a/environment.yml +++ b/environment.yml @@ -1,7 +1,7 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml # use this to find packages: https://anaconda.org/ -name: qbic-pipelines-rnadeseq-2.4 +name: qbic-pipelines-rnadeseq-2.5 channels: - bioconda - conda-forge diff --git a/modules/local/report.nf b/modules/local/report.nf index a67227f9..a3bf33e2 100644 --- a/modules/local/report.nf +++ b/modules/local/report.nf @@ -1,6 +1,6 @@ process REPORT { - container 'ghcr.io/qbic-pipelines/rnadeseq:2.4' + container 'ghcr.io/qbic-pipelines/rnadeseq:2.5' input: path gene_counts diff --git a/nextflow.config b/nextflow.config index b5a13834..bb0f314a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { description = """Differential gene expression analysis and pathway analysis of RNAseq data""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '2.4' + version = '2.5' doi = '' }