Merge pull request #244 from qbic-pipelines/dev

Release 2.3 - This time for real

.nf-core.yml

@@ -23,6 +23,8 @@ lint:
         - params.custom_config_base
         - params.report_file
         - params.references_file
+        - params.css
+        - params.logo
 
   multiqc_config:
     - report_comment # otherwise throws error: multiqc_config: 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## 2.3
+## 2.3 - Flowering Orchards
 
 ### Added
 
@@ -15,11 +15,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [#244](https://github.com/qbic-pipelines/rnadeseq/pull/244) Release 2.3 to master, part II (found a bug before actual release)
 - [#237](https://github.com/qbic-pipelines/rnadeseq/pull/237) Changed geom_jitter to geom_point for volcano plot so that points are accurate
+- [#233](https://github.com/qbic-pipelines/rnadeseq/pull/233) Release 2.3 to master, part I
 - [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Shortened names of some output files
 
 ### Fixed
 
+- [#243](https://github.com/qbic-pipelines/rnadeseq/pull/243) Fix missing QBiC logo and css styling in report by adding logo/css params
+- [#242](https://github.com/qbic-pipelines/rnadeseq/pull/242) Fix path issue in report by adding report_file/references_file params
 - [#241](https://github.com/qbic-pipelines/rnadeseq/pull/241) Undo fix branch protection bug in order to get precommit test to run
 - [#240](https://github.com/qbic-pipelines/rnadeseq/pull/240) Fix branch protection bug --> third attempt
 - [#239](https://github.com/qbic-pipelines/rnadeseq/pull/239) Fix branch protection bug --> second attempt
@@ -32,7 +36,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#225](https://github.com/qbic-pipelines/rnadeseq/pull/225) Fixed too many devices error from tryCatch around normalized heatmaps
 - [#221](https://github.com/qbic-pipelines/rnadeseq/pull/221) Fixed non-conformable arrays bug, fix wrong volcano colors when no DE genes
 
-## 2.2 Avenue of Poplars
+## 2.2 - Avenue of Poplars
 
 ### Added
 

assets/RNAseq_report.Rmd

@@ -52,6 +52,7 @@ params:
     path_quote: ''
     path_software_versions: ''
     revision: ''
+    logo: ''
 
     #Additional arg to indicate that a github test is run
     citest: ''
@@ -301,7 +302,12 @@ author: "`r PM`, Bioinformatics Research Scientist"
 date: '`r format(Sys.Date(), "%B %d, %Y")`'
 ---
 
-<img src="./logo.png" style="position:absolute;top:0px;right:0px;" height="200" width="200" />
+```{r logo, echo=FALSE, results='asis'}
+logo_file = file.path(getwd(), "logo.png")
+img_data <- base64enc::dataURI(file = logo_file, mime = "image/png") # Need to use base64 because the logo will otherwise for some reason not be loaded correctly
+cat(sprintf('<img src="%s" style="position:absolute;top:0px;right:0px;" height="200" width="200" />', img_data))
+```
+
 <div class="watermark">QBiC</div>
 
 ```{r docSetup, bootstrap.show.code = FALSE, dev = c('png'), bootstrap.show.message=FALSE, echo=FALSE, message=FALSE, warning=FALSE}
@@ -1027,7 +1033,7 @@ if (mqc_version == 'old_mqc') {
     table_complete <- table_complete %>%
         mutate(
             Sample = Sample,
-            ReadNumber = round((ReadNumber/1000000),2),
+            ReadNumber = color_bar("lightblue")(round((ReadNumber/1000000),2)),
             DuplicateReadsIntercept = ifelse(DuplicateReadsIntercept > 1,
                                             cell_spec(DuplicateReadsIntercept, color="orange", bold=T),
                                             cell_spec(DuplicateReadsIntercept, color="black")),

bin/Execute_report.R

@@ -42,6 +42,7 @@ option_list = list(
     make_option(c("--path_quote"), type="character", default=NULL, help="Path to the quote PDF", metavar="character"),
     make_option(c("-v", "--software_versions"), type="character", default=NULL, help="Versions file", metavar="character"),
     make_option(c("-j", "--revision"), type="character", default=NULL, help="Rnadeseq workflow revision", metavar="character"),
+    make_option("--logo", type="character", default=NULL, help="Logo image file", metavar="character"),
 
     make_option("--citest", action="store_true", default=FALSE, help="Run github test and don't save pathway heatmaps.")
 )
@@ -93,5 +94,6 @@ rmarkdown::render(opt$report, output_file = opt$output, knit_root_dir = wd, outp
                                 path_quote = opt$path_quote,
                                 path_software_versions = opt$software_versions,
                                 revision = opt$revision,
+                                logo = opt$logo,
 
                                 citest = opt$citest))

modules/local/report.nf

@@ -21,6 +21,8 @@ process REPORT {
     path custom_background
     path report_file
     path references_file
+    path css
+    path logo
 
     output:
     path "*.zip"
@@ -89,6 +91,7 @@ process REPORT {
         $software_versions_opt \
         --proj_summary $proj_summary \
         --revision $workflow.manifest.version \
+        --logo $logo \
         $citest_opt
 
     # Remove allgenes dir as the contained files do not contain only DE genes

nextflow.config

@@ -50,6 +50,8 @@ params {
     software_versions = 'NO_FILE6'
     report_file = "$projectDir/assets/RNAseq_report.Rmd"
     references_file = "$projectDir/assets/references.bibtex"
+    css = "$projectDir/assets/corp-styles.css"
+    logo = "$projectDir/assets/logo.png"
 
     // Additional arg to indicate that a github test is run
     citest = false

nextflow_schema.json

@@ -193,6 +193,16 @@
                     "type": "string",
                     "default": "${projectDir}/assets/references.bibtex",
                     "description": "Reference bibtex file for the report, should not be changed."
+                },
+                "css": {
+                    "type": "string",
+                    "default": "${projectDir}/assets/corp-styles.css",
+                    "description": "Stylesheet css file for the report, should not be changed."
+                },
+                "logo": {
+                    "type": "string",
+                    "default": "${projectDir}/assets/logo.png",
+                    "description": "QBiC logo png file for the report, should not be changed."
                 }
             }
         },

workflows/rnadeseq.nf

@@ -33,6 +33,8 @@ ch_proj_summary_file = Channel.fromPath(params.project_summary)
 ch_softwareversions_file = Channel.fromPath(params.software_versions)
 ch_report_file = Channel.fromPath(params.report_file)
 ch_references_file = Channel.fromPath(params.references_file)
+ch_css = Channel.fromPath(params.css)
+ch_logo = Channel.fromPath(params.logo)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -78,7 +80,9 @@ workflow RNADESEQ {
         ch_custom_gmt,
         ch_custom_background,
         ch_report_file,
-        ch_references_file
+        ch_references_file,
+        ch_css,
+        ch_logo
     )
 
     //TODO: Enable this: