diff --git a/inst/rmarkdown/templates/common/skeleton/README.md b/inst/rmarkdown/templates/common/skeleton/README.md new file mode 100644 index 0000000..30016c5 --- /dev/null +++ b/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 + diff --git a/inst/rmarkdown/templates/common/skeleton/code/placeholder.R b/inst/rmarkdown/templates/common/skeleton/code/placeholder.R new file mode 100644 index 0000000..e69de29 diff --git a/inst/rmarkdown/templates/common/skeleton/data/readme b/inst/rmarkdown/templates/common/skeleton/data/readme new file mode 100644 index 0000000..e69de29 diff --git a/inst/rmarkdown/templates/common/skeleton/information.R b/inst/rmarkdown/templates/common/skeleton/information.R new file mode 100644 index 0000000..6e15eef --- /dev/null +++ b/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' diff --git a/inst/rmarkdown/templates/common/skeleton/scripts/placeholder b/inst/rmarkdown/templates/common/skeleton/scripts/placeholder new file mode 100644 index 0000000..e69de29 diff --git a/inst/rmarkdown/templates/common/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/common/skeleton/skeleton.Rmd new file mode 100644 index 0000000..dc4bbf5 --- /dev/null +++ b/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) +``` diff --git a/inst/rmarkdown/templates/common/template.yaml b/inst/rmarkdown/templates/common/template.yaml new file mode 100644 index 0000000..1db494c --- /dev/null +++ b/inst/rmarkdown/templates/common/template.yaml @@ -0,0 +1,3 @@ +name: bcbio base +description: Standard NGS down-stream analyses +create_dir: true