Merge pull request #79 from ggabernet/bugfix

Bugfix boxplots requested genes

Author: ggabernet

.github/workflows/ci.yml

@@ -31,13 +31,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:1.3.1
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.3.1
 
       - name: Install Nextflow
         run: |
@@ -69,13 +69,13 @@ jobs:
       
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t qbicpipelines/rnadeseq:dev
+        run: docker build --no-cache . -t qbicpipelines/rnadeseq:1.3.1
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull qbicpipelines/rnadeseq:dev
-          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:dev
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.3.1
 
       - name: Install Nextflow
         run: |

CHANGELOG.md

@@ -1,10 +1,10 @@
 # qbic-pipelines/rnadeseq: Changelog
 
-## 1.3.1 - dev
+## 1.3.1 - Almond Blossoms hotfix
 
 ### Added
 
-- Bump versions to 1.3.1dev
+- Bump versions to 1.3.1
 
 ### Fixed
 

Dockerfile

@@ -9,10 +9,10 @@ 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-1.3.1dev/bin:$PATH
+ENV PATH /opt/conda/envs/qbic-pipelines-rnadeseq-1.3.1/bin:$PATH
 
 # Dump the details of the installed packates to a file for posterity
-RUN conda env export --name qbic-pipelines-rnadeseq-1.3.1dev > qbic-pipelines-rnadeseq-1.3.1dev.yml
+RUN conda env export --name qbic-pipelines-rnadeseq-1.3.1 > qbic-pipelines-rnadeseq-1.3.1.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local config
 RUN touch .Rprofile

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-1.3.1dev
+name: qbic-pipelines-rnadeseq-1.3.1
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -46,7 +46,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'qbicpipelines/rnadeseq:dev'
+process.container = 'qbicpipelines/rnadeseq:1.3.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -102,7 +102,7 @@ manifest {
   description = 'Downstream differential gene expression analysis with DESeq2'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.04'
-  version = '1.3.1dev'
+  version = '1.3.1'
 }
 
 // Function to ensure that resource requirements don't go beyond