diff --git a/.nf-core.yml b/.nf-core.yml
index ee90d841..86cdab14 100644
--- a/.nf-core.yml
+++ b/.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'.
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 039ed3dc..7cab29c3 100644
--- a/CHANGELOG.md
+++ b/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
+- [#243](https://github.com/qbic-pipelines/rnadeseq/pull/243) 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
diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd
index 9e66e7d4..72482212 100644
--- a/assets/RNAseq_report.Rmd
+++ b/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")`'
---
-
+```{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_data))
+```
+
QBiC
```{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")),
diff --git a/bin/Execute_report.R b/bin/Execute_report.R
index 574fbc1e..21d2ad93 100755
--- a/bin/Execute_report.R
+++ b/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))
diff --git a/modules/local/report.nf b/modules/local/report.nf
index 5c0fcab1..05e10831 100644
--- a/modules/local/report.nf
+++ b/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 \
$citest_opt
# Remove allgenes dir as the contained files do not contain only DE genes
diff --git a/nextflow.config b/nextflow.config
index 8db8337c..faf95d30 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -50,6 +50,8 @@ params {
software_versions = 'NO_FILE6'
report_file = "$projectDir/assets/RNAseq_report.Rmd"
references_file = "$projectDir/assets/references.bibtex"
+ css = "$projectDir/assets/corp-styles.css"
+ logo = "$projectDir/assets/logo.png"
// Additional arg to indicate that a github test is run
citest = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index aa6b89a2..33f48902 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -193,6 +193,16 @@
"type": "string",
"default": "${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."
}
}
},
diff --git a/workflows/rnadeseq.nf b/workflows/rnadeseq.nf
index ead6be2a..6f11e26d 100644
--- a/workflows/rnadeseq.nf
+++ b/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: