1) Fix enriched pathways display error in report

.github/workflows/ci.yml

@@ -36,13 +36,13 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
@@ -88,13 +88,13 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:2.1
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:2.1
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

CHANGELOG.md

@@ -3,6 +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).
 
+## 2.1dev
+
+### Added
+
+### Changed
+
+### Fixed
+
+- [#195](https://github.com/qbic-pipelines/rnadeseq/pull/195) Fixed section error in report
+
 ## 2.1 - Wheat Fields
 
 ### Added

Dockerfile

@@ -3,14 +3,14 @@ LABEL authors="Gisela Gabernet, Alexander Peltzer" \
     description="Docker image containing all requirements for qbic-pipelines/rnadeseq pipeline"
 COPY environment.yml /
 #RUN conda install -c conda-forge mamba
-RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-2.1 && \
+RUN mamba env create --file /environment.yml -p /opt/conda/envs/qbic-pipelines-rnadeseq-dev && \
     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-2.1/bin:$PATH
+ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-dev/bin:$PATH
 # Dump the details of the installed packates to a file for posterity
-RUN mamba env export --name qbic-pipelines-rnadeseq-2.1 > qbic-pipelines-rnadeseq-2.1.yml
+RUN mamba env export --name qbic-pipelines-rnadeseq-dev > qbic-pipelines-rnadeseq-dev.yml
 # Instruct R processes to use these empty files instead of clashing with a local config
 RUN touch .Rprofile
 RUN touch .Renviron

assets/RNAseq_report.Rmd

@@ -1883,7 +1883,7 @@ Inside the pathway analysis results folder, a subfolder for each contrast used f
 </details><br>",
 gost_text,
 
-"
+"\n
 ## Enriched pathways
 The plot below summarizes the pathways that were
 found significantly enriched in DE genes for each contrast (padj value < ", pval_text, ").

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-2.1
+name: qbic-pipelines-rnadeseq-dev
 channels:
   - bioconda
   - conda-forge

modules/local/report.nf

@@ -1,6 +1,6 @@
 process REPORT {
 
-    container 'qbicpipelines/rnadeseq:2.1'
+    container 'qbicpipelines/rnadeseq:dev'
 
     input:
     path gene_counts