Merge pull request #135 from bcbio/devel

fix readme

Author: lpantano

.github/workflows/release.yaml

@@ -29,7 +29,7 @@ jobs:
         patch=0
 
         # Get commit messages from last release tag to HEAD
-        commits=$(git log ${GITHUB_ENV[latest_tag]..HEAD --oneline --pretty=%B)
+        commits=$(git log ${GITHUB_ENV[latest_tag]..HEAD} --oneline --pretty=%B)
 
         for commit in $commits; do
           if [[ "$commit" == *"BREAKING CHANGE"* ]]; then

R/helpers.R

@@ -212,6 +212,8 @@ copy_templates <- function(path, pipeline, org=NULL){
     names(repos)="rnaseq-reports"
   }else if(pipeline=="singlecell"){
     parts = c("templates/singlecell")
+    # repos = "https://github.com/bcbio/singlecell-reports"
+    # names(repos)="singlecell-reports"
     apps=c(apps, scRNAseq_qc="https://github.com/hbc/scRNAseq_qc_app/archive/refs/heads/main.zip")
   }else if(pipeline=="singlecell_delux"){
     parts = c("templates/singlecell_delux")

README.md

@@ -44,14 +44,16 @@ bcbio_templates(type="rnaseq", outpath="/path/to/analysis/folder/reports")
 ## Supported analyses
 
 - base/reports/example.Rmd: ![](https://img.shields.io/badge/status-stable-green)
-- [rnaseq/01_quality_assessment/QC.Rmd](rnaseq/01_quality_assessment/QC.Rmd): ![](https://img.shields.io/badge/status-stable-green)
-- [rnaseq/02_differential_expression/DEG.Rmd](rnaseq/02_differential_expression/DEG.Rmd): ![](https://img.shields.io/badge/status-stable-green)
-- [rnaseq/03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd](rnaseq/03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [rnaseq/03_functional/GSVA.Rmd](rnaseq/03_functional/GSVA.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [rnaseq/03_functional/Immune-deconvolution.Rmd](rnaseq/03_functional/Immune-deconvolution.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [rnaseq/03_comparative/Pair-wise-comparison-analysis.Rmd](rnaseq/03_comparative/Pair-wise-comparison-analysis.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [rnaseq/03_comparative/Intersections.Rmd](rnaseq/03_comparative/Intersections.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
-- [rnaseq/04_gene_patterns/WGCNA.Rmd](rnaseq/04_gene_patterns/WGCNA.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)
+- [rnaseq-reports](https://github.com/bcbio/rnaseq-reports):
+  - 01_quality_assessment/QC.Rmd: ![](https://img.shields.io/badge/status-stable-green)
+  - 02_differential_expression/DEG.Rmd: ![](https://img.shields.io/badge/status-stable-green)
+  - 03_functional/Nonmodel_Organism_Pathway_Analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+  - 03_functional/GSVA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+  - 03_functional/Immune-deconvolution.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+  - 03_comparative/Pair-wise-comparison-analysis.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+  - 03_comparative/Intersections.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+  - 04_gene_patterns/WGCNA.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
+  - 05_gene_patterns/DEGpattern.Rmd: ![](https://img.shields.io/badge/status-alpha-yellow)
 - [singlecell/01_quality_assessment/scRNA_QC.Rmd](singlecell/01_quality_assessment/scATAC_QC.Rmd): ![](https://img.shields.io/badge/status-stable-green)
 - [singlecell/01_quality_assessment/scATAC_QC.Rmd](singlecell/01_quality_assessment/scATAC_QC.Rmd): ![](https://img.shields.io/badge/status-draft-grey)
 - [singlecell/02_differential_expression/scRNA_MAST.Rmd](singlecell/02_differential_expression/scRNA_MAST.Rmd): ![](https://img.shields.io/badge/status-alpha-yellow)