Merge pull request #259 from WackerO/bump_versions

Bump versions for release 2.5

.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

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
 

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

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

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

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             = ''
 }