add common files of a project

inst/rmarkdown/templates/common/skeleton/README.md

@@ -0,0 +1,13 @@
+# TODO
+
+[ ] Replace Title in this file matching title projects
+[ ] run function`bcbio_set_project()` to set up information for this project
+    - hbcxxxx code
+    - technology
+    - tissue
+    - organism
+    - pi
+    - project name
+[ ] run function `bcbio_set_git()` to set up git repository
+[ ] run function `bcbio_copy_dropbox()` to copy files to dropbox location
+

inst/rmarkdown/templates/common/skeleton/information.R

@@ -0,0 +1,6 @@
+# info params
+project = "name_hbcXXXXX"
+PI = 'person name'
+experiment = 'short description'
+aim = 'short description'
+analyst = 'person in the core'

inst/rmarkdown/templates/common/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: information.R
+---
+
+```{r echo = F}
+source(params$params_file)
+```

inst/rmarkdown/templates/common/template.yaml

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