Merge pull request #80 from qbic-pipelines/release

Release1.3.1

.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:1.3.0
+        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:1.3.0
+          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:1.3.0
+        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:1.3.0
+          docker tag qbicpipelines/rnadeseq:dev qbicpipelines/rnadeseq:1.3.1
 
       - name: Install Nextflow
         run: |

CHANGELOG.md

@@ -1,5 +1,17 @@
 # qbic-pipelines/rnadeseq: Changelog
 
+## 1.3.1 - Almond Blossoms hotfix
+
+### Added
+
+- Bump versions to 1.3.1
+
+### Fixed
+
+- Fix bug plots requested boxplots
+
+### Changed
+
 ## 1.3.0 - Almond Blossoms
 
 ### Added

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-1.3.0/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-1.3.0 > qbic-pipelines-rnadeseq-1.3.0.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

bin/DESeq2.R

@@ -205,6 +205,7 @@ if (!is.null(opt$contrasts_matrix)){
 
     contname <- names(contrasts[i])
     results_DEseq_contrast <- as.data.frame(results_DEseq_contrast)
+    print("Analyzing contrast:")
     print(contname)
     # Add gene name in table
     DE_genes_contrast_genename <- results_DEseq_contrast
@@ -268,6 +269,7 @@ if (!is.null(opt$contrasts_pairs)) {
       } 
       results_DEseq_contrast <- results(cds, contrast=list(cont[1],cont[2]))
       results_DEseq_contrast <- as.data.frame(results_DEseq_contrast)
+      print("Analyzing contrast:")
       print(contname)
       # Add gene name in table
       DE_genes_contrast_genename <- results_DEseq_contrast
@@ -294,6 +296,7 @@ if (is.null(opt$contrasts_matrix) & is.null(opt$contrasts_list) & is.null(opt$co
   for (contname in contrast_names) {
     results_DEseq_contrast <- results(cds, name=contname)
     results_DEseq_contrast <- as.data.frame(results_DEseq_contrast)
+    print("Analyzing contrast:")
     print(contname)
 
     # Adding gene name to table
@@ -413,12 +416,13 @@ if (!is.null(opt$genelist)){
   requested_genes_plot <- subset(gene_names, gene_name %in% gene_ids$requested_gene_name)
 
   # Check that genes are in the cds table
-  requested_genes_plot <- requested_genes_plot[which(requested_genes_plot$Ensemble_ID %in% row.names(cds)),]
+  requested_genes_plot <- subset(requested_genes_plot, requested_genes_plot$Ensembl_ID %in% row.names(cds))
+
   requested_genes_plot_Ensembl <- requested_genes_plot$Ensembl_ID
   requested_genes_plot_gene_name <- requested_genes_plot$gene_name
 
-  for (i in requested_genes_plot_Ensembl){
-    boxplot_counts <- plotCounts(cds, gene=i, intgroup=c("combfactor"), returnData=TRUE, normalized = T)
+  for (i in c(1:length(requested_genes_plot_Ensembl))){
+    boxplot_counts <- plotCounts(cds, gene=requested_genes_plot_Ensembl[i], intgroup=c("combfactor"), returnData=TRUE, normalized = T)
     boxplot_counts$variable = row.names(boxplot_counts)
     plot <- ggplot(data=boxplot_counts, aes(x=combfactor, y=count, fill=combfactor)) +
       geom_boxplot(position=position_dodge()) +

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-1.3.0
+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:1.3.0'
+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 = '1.3.0'
+  version = '1.3.1'
 }
 
 // Function to ensure that resource requirements don't go beyond