reorg rnaseq project

R/hello.R

@@ -1,6 +1,6 @@
 # Hello, world!
 #
-# This is an example function named 'hello' 
+# This is an example function named 'hello'
 # which prints 'Hello, world!'.
 #
 # You can learn more about package authoring with RStudio at:
@@ -15,4 +15,5 @@
 
 hello <- function() {
   print("Hello, world!")
+
 }

inst/rmarkdown/templates/rnaseq_qc/skeleton/skeleton.Rmd → inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/DEG.Rmd

@@ -21,7 +21,6 @@ params:
   denominator: bar
   subset_value: nah
   params_file: params_de.R
-
 ---
 
 ```{r echo = F}

inst/rmarkdown/templates/rnaseq/skeleton/skeleton.Rmd

@@ -0,0 +1,25 @@
+---
+title: "General Project Information"
+author: "Harvard Chan Bioinformatics Core"
+date: "`r Sys.Date()`"
+output:
+   html_document:
+      code_folding: hide
+      df_print: paged
+      highlights: pygments
+      number_sections: true
+      self_contained: true
+      theme: default
+      toc: true
+      toc_float:
+         collapsed: true
+         smooth_scroll: true
+editor_options: 
+  chunk_output_type: console
+params:
+  params_file: params_de.R
+---
+
+```{r echo = F}
+source(params$params_file)
+```

inst/rmarkdown/templates/rnaseq/template.yaml

@@ -0,0 +1,3 @@
+name: bcbio RNAseq
+description: Standard RNAseq down-stream analyses
+create_dir: true