Merge pull request qbic-pipelines#249 from qbic-pipelines/dev

Release 2.4

.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

@@ -3,6 +3,22 @@
 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).
 
+## 2.4 - 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
+
+- [#247](https://github.com/qbic-pipelines/rnadeseq/pull/247) Removed hard-coded comment about usage of gprofiler databases KEGG and REAC in the report
+
 ## 2.3 - Flowering Orchards
 
 ### Added

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-2.3 && \
+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-2.3/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-2.3 > qbic-pipelines-rnadeseq-2.3.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

assets/RNAseq_report.Rmd

@@ -1969,13 +1969,15 @@ if (isProvided(params$datasources)) {
 min_DEG_pathway <- as.integer(params$min_DEG_pathway)
 
 # If background list is to be used, load custom background list
-# if provided, else use notAllZero
+# if provided, else use notAllZero -->then save to output
 if (isProvided(params$set_background)) {
     if (isProvided(params$custom_background)) {
         custom_background <- readLines(params$custom_background)
     } else {
         custom_background <- rownames(counts(cds))[notAllZero]
     }
+    dir.create("pathway_analysis/metadata")
+    write.table(custom_background, "pathway_analysis/metadata/custom_background.txt", quote=F, row.names = F, col.names = F)
 }
 
 # Contrast files
@@ -2368,14 +2370,20 @@ if (isProvided(params$path_genelist)){
 
 ```{r pathway_analysis, echo=FALSE, results='asis', eval=params$pathway_analysis}
 
+if (isProvided(params$set_background)) {
+    background_list_text <- "The background gene list used for pathway analysis is saved [here](./pathway_analysis/metadata/custom_background.txt)"
+} else {
+    background_list_text <- ""
+}
+
 if (mv_status) {
     if (isProvided(params$custom_gmt)) {
         gost_text <- "A custom GMT file was provided for the gost query; it is saved [here](./pathway_analysis/metadata). In case this GMT file contained entries from datasources other than the selected ones, it was filtered and the resulting filtered GMT was used for querying. The filtered version is also saved to the metadata folder."
     } else {
         gost_text <- "A GMT file corresponding to the current gprofiler database version was downloaded to allow for reproducing the gost query; it is saved [here](./pathway_analysis/metadata). Note that the downloaded GMT contains entries from various datasources, not just the selected ones. Also, some datasources might be missing from the files due to licensing reasons."
     }
 } else {
-    gost_text <- paste0("Failed to fetch the GMT file of the current gprofiler database with this URL: ", gmt_url, ". For reproducibility reasons, try to download the GMT file manually by visiting https://biit.cs.ut.ee/gprofiler/gost, then selecting the correct organism and finally, in datasources, clicking 'combined ENSG.gmt'.")
+    gost_text <- paste0("The GMT file of the current gprofiler database could not be downloaded with this URL: ", gmt_url, ". For reproducibility reasons, try to download the GMT file manually by visiting https://biit.cs.ut.ee/gprofiler/gost, then selecting the correct organism and finally, in datasources, clicking 'combined ENSG.gmt'.")
 }
 
 # The following details block creates a collapsible explaining the output folders/files
@@ -2404,7 +2412,7 @@ 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, ").
-Only contrasts for which an enriched pathway was found are shown. Both KEGG pathways and REACTOME (REAC) pathways are considered.
+Only contrasts for which an enriched pathway was found are shown.
 Hover over the dots to reveal the pathway names. The table below provides more detail on all enriched pathways."))
 ```
 

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-2.3
+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:2.3'
+    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         = '2.3'
+    version         = '2.4'
     doi             = ''
 }