From 984b2b6745d59e31a2da6e85ab34d0030a2547bc Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Fri, 19 Apr 2024 08:58:16 -0400
Subject: [PATCH 1/2] add common files of a project

---
 .../templates/common/skeleton/README.md       | 13 ++++++++++
 .../common/skeleton/code/placeholder.R        |  0
 .../templates/common/skeleton/data/readme     |  0
 .../templates/common/skeleton/information.R   |  6 +++++
 .../common/skeleton/scripts/placeholder       |  0
 .../templates/common/skeleton/skeleton.Rmd    | 25 +++++++++++++++++++
 inst/rmarkdown/templates/common/template.yaml |  3 +++
 7 files changed, 47 insertions(+)
 create mode 100644 inst/rmarkdown/templates/common/skeleton/README.md
 create mode 100644 inst/rmarkdown/templates/common/skeleton/code/placeholder.R
 create mode 100644 inst/rmarkdown/templates/common/skeleton/data/readme
 create mode 100644 inst/rmarkdown/templates/common/skeleton/information.R
 create mode 100644 inst/rmarkdown/templates/common/skeleton/scripts/placeholder
 create mode 100644 inst/rmarkdown/templates/common/skeleton/skeleton.Rmd
 create mode 100644 inst/rmarkdown/templates/common/template.yaml

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

From 20c012759deb9ebb91651a7d3019e4a7cafba3af Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Fri, 19 Apr 2024 09:08:07 -0400
Subject: [PATCH 2/2] fix start function

---
 R/hello.R | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/R/hello.R b/R/hello.R
index e148037..7e90f7f 100644
--- a/R/hello.R
+++ b/R/hello.R
@@ -14,26 +14,27 @@
 #   Test Package:              'Cmd + Shift + T'
 
 .fix <- function(x){
-  x <- tolower(x) %>% str_replace_all(x, "[[:punct:]]", " ")
-  retunr(x)
+  x <- tolower(x) %>% str_replace_all(., "[[:punct:]]", "_")
+  return(x)
 }
 
 #' @export
 bcbio_set_project <- function() {
   hbc_code <- readline("What is the hbc code:\n")
+  hbc_code <- paste0("hbc", hbc_code)
   pi <- readline("What is PI last name:\n")
   technology <- readline("What is the technology:\n")
   tissue <- readline("What is the tissue:\n")
   org <- readline("What is the organism:\n")
   project <- readline("What is the project name:\n")
-  dropbox <- readline("What is the dropbox name:\n")
-  github_org <- readline("What is the github organization:\n")
+  #dropbox <- readline("What is the dropbox name:\n")
+  #github_org <- readline("What is the github organization:\n")
   #hbc_$technology_of_$pilastname_$intervention_on_$tissue_in_$organism_$hbccode
-  project_full <- paste(project, technology, fix(pi), project, tissue, organism, hbc_code, sep="_")
-  github <- c(github_org,project_full)
-  opts <- list(code=hbc_code, project=project_full,
-               dropbox=file.path(dropbox,project_full),
-               github=github)
+  project_full <- paste(technology, .fix(pi), .fix(project), tissue, org, hbc_code, sep="_")
+  #github <- c(github_org,project_full)
+  opts <- list(code=hbc_code, project=project_full)
+               #dropbox=file.path(dropbox,project_full),
+               #github=github)
   print(opts)
   return(opts)
 }