Merge pull request #248 from WackerO/versions_2_4

4 - Bumped versions to 2.4 for next release

Author: WackerO

.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:2.3
+        run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.4
 
       # 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:2.3
+          docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.4
 
       - 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:2.3
+        run: docker build --no-cache . -t ghcr.io/qbic-pipelines/rnadeseq:2.4
 
       # 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:2.3
+          docker tag ghcr.io/qbic-pipelines/rnadeseq:dev ghcr.io/qbic-pipelines/rnadeseq:2.4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

CHANGELOG.md

@@ -3,14 +3,16 @@
 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
+## 2.4 - A Pair of Shoes
 
 ### Added
 
 - [#245](https://github.com/qbic-pipelines/rnadeseq/pull/245) Added background gene list to pathway analysis output
 
 ### Changed
 
+- [#249](https://github.com/qbic-pipelines/rnadeseq/pull/249) Release 2.4
+- [#248](https://github.com/qbic-pipelines/rnadeseq/pull/248) Version bumps for release 2.4
 - [#247](https://github.com/qbic-pipelines/rnadeseq/pull/247) Changed the report text that shows when the gprofiler GMT file could not be downloaded
 
 ### Removed

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-dev && \
+RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.4 && \
     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-dev/bin:$PATH
+ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-2.4/bin:$PATH
 # Dump the details of the installed packates to a file for posterity
-RUN mamba env export --name qbic-pipelines-rnadeseq-dev > qbic-pipelines-rnadeseq-dev.yml
+RUN mamba env export --name qbic-pipelines-rnadeseq-2.4 > qbic-pipelines-rnadeseq-2.4.yml
 # Instruct R processes to use these empty files instead of clashing with a local config
 RUN touch .Rprofile
 RUN touch .Renviron

docs/usage.md

@@ -89,7 +89,7 @@ The `qbic-pipelines/rnadeseq` pipeline relies on the output from the `nf-core/rn
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run qbic-pipelines/rnadeseq -r 2.3 -profile docker \
+nextflow run qbic-pipelines/rnadeseq -r 2.4 -profile docker \
 --gene_counts 'merged_gene_counts.txt' \
 --input 'QXXXX_sample_preparations.tsv' \
 --model 'linear_model.txt' \
@@ -157,7 +157,7 @@ curl https://codeload.github.com/qbic-pipelines/rnadeseq/tar.gz/master | tar -xz
 Afterwards, you should be able to also run test_star_rsem and test_star_salmon from qbic-pipelines/rnadeseq without manually cloning, e.g.:
 
 ```bash
-nextflow run qbic-pipelines/rnadeseq -r 2.3 -profile docker,test_star_salmon
+nextflow run qbic-pipelines/rnadeseq -r 2.4 -profile docker,test_star_salmon
 ```
 
 ### Reproducibility

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-dev
+name: qbic-pipelines-rnadeseq-2.4
 channels:
   - bioconda
   - conda-forge

modules/local/report.nf

@@ -1,6 +1,6 @@
 process REPORT {
 
-    container 'ghcr.io/qbic-pipelines/rnadeseq:dev'
+    container 'ghcr.io/qbic-pipelines/rnadeseq:2.4'
 
     input:
     path gene_counts

nextflow.config

@@ -276,7 +276,7 @@ manifest {
     description     = """Differential gene expression analysis and pathway analysis of RNAseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = 'dev'
+    version         = '2.4'
     doi             = ''
 }