From a055d97c8decf3268217dd5baa15d2dab34977f3 Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Wed, 17 Apr 2024 14:59:27 -0400
Subject: [PATCH] reorg rnaseq project

---
 R/hello.R                                     |  3 ++-
 .../skeleton/params_de.R                      |  0
 .../skeleton/reports/DEG/DEG.Rmd}             |  1 -
 .../templates/rnaseq/skeleton/skeleton.Rmd    | 25 +++++++++++++++++++
 inst/rmarkdown/templates/rnaseq/template.yaml |  3 +++
 .../templates/rnaseq_qc/template.yaml         |  3 ---
 6 files changed, 30 insertions(+), 5 deletions(-)
 rename inst/rmarkdown/templates/{rnaseq_qc => rnaseq}/skeleton/params_de.R (100%)
 rename inst/rmarkdown/templates/{rnaseq_qc/skeleton/skeleton.Rmd => rnaseq/skeleton/reports/DEG/DEG.Rmd} (99%)
 create mode 100644 inst/rmarkdown/templates/rnaseq/skeleton/skeleton.Rmd
 create mode 100644 inst/rmarkdown/templates/rnaseq/template.yaml
 delete mode 100644 inst/rmarkdown/templates/rnaseq_qc/template.yaml

diff --git a/R/hello.R b/R/hello.R
index 3d348f2..c61eb13 100644
--- a/R/hello.R
+++ b/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!")
+
 }
diff --git a/inst/rmarkdown/templates/rnaseq_qc/skeleton/params_de.R b/inst/rmarkdown/templates/rnaseq/skeleton/params_de.R
similarity index 100%
rename from inst/rmarkdown/templates/rnaseq_qc/skeleton/params_de.R
rename to inst/rmarkdown/templates/rnaseq/skeleton/params_de.R
diff --git a/inst/rmarkdown/templates/rnaseq_qc/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/DEG.Rmd
similarity index 99%
rename from inst/rmarkdown/templates/rnaseq_qc/skeleton/skeleton.Rmd
rename to inst/rmarkdown/templates/rnaseq/skeleton/reports/DEG/DEG.Rmd
index 4185d70..313d9d5 100644
--- a/inst/rmarkdown/templates/rnaseq_qc/skeleton/skeleton.Rmd
+++ b/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}
diff --git a/inst/rmarkdown/templates/rnaseq/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/rnaseq/skeleton/skeleton.Rmd
new file mode 100644
index 0000000..115b32b
--- /dev/null
+++ b/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)
+```
diff --git a/inst/rmarkdown/templates/rnaseq/template.yaml b/inst/rmarkdown/templates/rnaseq/template.yaml
new file mode 100644
index 0000000..9f35cf7
--- /dev/null
+++ b/inst/rmarkdown/templates/rnaseq/template.yaml
@@ -0,0 +1,3 @@
+name: bcbio RNAseq
+description: Standard RNAseq down-stream analyses
+create_dir: true
diff --git a/inst/rmarkdown/templates/rnaseq_qc/template.yaml b/inst/rmarkdown/templates/rnaseq_qc/template.yaml
deleted file mode 100644
index db9e4aa..0000000
--- a/inst/rmarkdown/templates/rnaseq_qc/template.yaml
+++ /dev/null
@@ -1,3 +0,0 @@
-name: bcbio RNAseq QC
-description: Standard RNAseq QC after running bcbio
-create_dir: true