use repositories now

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: bcbioR
 Type: Package
 Title: Templates and functions to guide downstream analysis and data interpretation
-Version: 0.4.4
+Version: 0.4.5
 Authors@R: person("Pantano", "Lorena", , "lorena.pantano@gmail.com",
             role = c("aut", "cre"))
 Description: Collaborative code repository at the Harvard Chan Bioinformatics Core.

NEWS.md

@@ -1,3 +1,8 @@
+# bcbioR 0.4.5
+
+Migrate templates to bcbio individual repositories
+Add mm39 rRNA and tRNA annotation
+
 # bcbioR 0.4.4
 
 init QC single cell adding init file for params for single QC #123

R/helpers.R

@@ -83,17 +83,17 @@ bcbio_templates <- function(type="rnaseq", outpath=NULL, org=NULL){
            #file.copy(fpath, outpath, recursive = T)
            copy_templates(outpath, "spatial", org)
          },
-         chipseq={
+         peakseq={
            #file.copy(fpath, outpath, recursive = T)
-           copy_templates(outpath, "chipseq", org)
+           copy_templates(outpath, "peakseq", org)
          },
          multiomics={
            #file.copy(fpath, outpath, recursive = T)
            copy_templates(outpath, "multiomics", org)
          },
          {
            stop(paste('project type not recognize, please choose: ',
-                      'rnaseq', 'chipseq',
+                      'rnaseq', 'peakseq',
                       'singlecell','singlecell_delux','spatial'))
          }
   )
@@ -220,10 +220,14 @@ copy_templates <- function(path, pipeline, org=NULL){
   }else if(pipeline=="multiomics"){
     parts = c("templates/multiomics")
   }else if(pipeline=="spatial"){
-    parts = c("templates/spatial")
+    # parts = c("templates/spatial")
+    repos = "https://github.com/bcbio/spatial-reports/archive/refs/heads/main.zip"
+    names(repos)="spatial-reports"
     # apps=c(apps, SpatialViz="https://github.com/hbc/RShiny_app-SpatialViz/archive/refs/tags/Latest.zip")
-  }else if(pipeline=="chipseq"){
-    parts = c("templates/chipseq")
+  }else if(pipeline=="peakseq"){
+    # parts = c("templates/chipseq") #https://github.com/bcbio/peakseq-reports
+    repos = "https://github.com/bcbio/peakseq-reports/archive/refs/heads/main.zip"
+    names(repos)="peakseq-reports"
   }
 
   #check if it is url or folder