From 77a8624a34a9a60d29cafec0b27cd390c48ac57c Mon Sep 17 00:00:00 2001
From: Lorena Pantano <lorena.pantano@gmail.com>
Date: Wed, 24 Apr 2024 13:53:00 -0400
Subject: [PATCH] fix minor bugs in test data

---
 .../templates/{rnaseqv2 => rnaseq}/skeleton/DE/DEG.Rmd       | 5 +++--
 .../templates/{rnaseqv2 => rnaseq}/skeleton/DE/params_de.R   | 0
 .../{rnaseqv2 => rnaseq}/skeleton/DE/run_markdown.R          | 0
 .../templates/{rnaseqv2 => rnaseq}/skeleton/QC/QC.Rmd        | 0
 .../templates/{rnaseqv2 => rnaseq}/skeleton/QC/params_qc.R   | 0
 .../templates/rnaseq/skeleton/{results => QC}/placeholder    | 0
 .../{rnaseqv2 => rnaseq}/skeleton/QC/run_markdown.R          | 0
 .../templates/{rnaseqv2 => rnaseq}/skeleton/README.md        | 0
 .../templates/{rnaseqv2 => rnaseq}/skeleton/information.R    | 0
 .../templates/{rnaseqv2 => rnaseq}/skeleton/skeleton.Rmd     | 0
 inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/template.yaml  | 0
 inst/rmarkdown/templates/rnaseqv2/skeleton/QC/placeholder    | 0
 12 files changed, 3 insertions(+), 2 deletions(-)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/DE/DEG.Rmd (99%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/DE/params_de.R (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/DE/run_markdown.R (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/QC/QC.Rmd (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/QC/params_qc.R (100%)
 rename inst/rmarkdown/templates/rnaseq/skeleton/{results => QC}/placeholder (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/QC/run_markdown.R (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/README.md (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/information.R (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/skeleton/skeleton.Rmd (100%)
 rename inst/rmarkdown/templates/{rnaseqv2 => rnaseq}/template.yaml (100%)
 delete mode 100644 inst/rmarkdown/templates/rnaseqv2/skeleton/QC/placeholder

diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/DE/DEG.Rmd b/inst/rmarkdown/templates/rnaseq/skeleton/DE/DEG.Rmd
similarity index 99%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/DE/DEG.Rmd
rename to inst/rmarkdown/templates/rnaseq/skeleton/DE/DEG.Rmd
index c517ed3..0450da9 100644
--- a/inst/rmarkdown/templates/rnaseqv2/skeleton/DE/DEG.Rmd
+++ b/inst/rmarkdown/templates/rnaseq/skeleton/DE/DEG.Rmd
@@ -21,6 +21,7 @@ params:
   denominator: normal
   subset_value: NA
   params_file: params_de.R
+  project_file: ../information.R
 ---
 
 ```{r load_params, echo = F}
@@ -54,7 +55,7 @@ opts_chunk[["set"]](
     prompt = FALSE,
     tidy = FALSE,
     warning = FALSE,
-    echo = F, 
+    echo = T, 
     fig.height = 4)
 ```
 
@@ -332,7 +333,7 @@ res_for_writing <- res %>%
 pathways_for_writing <- pathways_long %>% 
   mutate(comparison = str_interp("${params$numerator}_vs_${params$denominator}"))
          
-if (!is.na(subset_value)){
+if (!is.na(params$subset_value)){
   counts_norm <- counts_norm %>% 
     mutate(subset = params$subset_value)  
   res_for_writing <- res_for_writing %>% 
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/DE/params_de.R b/inst/rmarkdown/templates/rnaseq/skeleton/DE/params_de.R
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/DE/params_de.R
rename to inst/rmarkdown/templates/rnaseq/skeleton/DE/params_de.R
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/DE/run_markdown.R b/inst/rmarkdown/templates/rnaseq/skeleton/DE/run_markdown.R
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/DE/run_markdown.R
rename to inst/rmarkdown/templates/rnaseq/skeleton/DE/run_markdown.R
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/QC/QC.Rmd b/inst/rmarkdown/templates/rnaseq/skeleton/QC/QC.Rmd
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/QC/QC.Rmd
rename to inst/rmarkdown/templates/rnaseq/skeleton/QC/QC.Rmd
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/QC/params_qc.R b/inst/rmarkdown/templates/rnaseq/skeleton/QC/params_qc.R
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/QC/params_qc.R
rename to inst/rmarkdown/templates/rnaseq/skeleton/QC/params_qc.R
diff --git a/inst/rmarkdown/templates/rnaseq/skeleton/results/placeholder b/inst/rmarkdown/templates/rnaseq/skeleton/QC/placeholder
similarity index 100%
rename from inst/rmarkdown/templates/rnaseq/skeleton/results/placeholder
rename to inst/rmarkdown/templates/rnaseq/skeleton/QC/placeholder
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/QC/run_markdown.R b/inst/rmarkdown/templates/rnaseq/skeleton/QC/run_markdown.R
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/QC/run_markdown.R
rename to inst/rmarkdown/templates/rnaseq/skeleton/QC/run_markdown.R
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/README.md b/inst/rmarkdown/templates/rnaseq/skeleton/README.md
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/README.md
rename to inst/rmarkdown/templates/rnaseq/skeleton/README.md
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/information.R b/inst/rmarkdown/templates/rnaseq/skeleton/information.R
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/information.R
rename to inst/rmarkdown/templates/rnaseq/skeleton/information.R
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/rnaseq/skeleton/skeleton.Rmd
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/skeleton/skeleton.Rmd
rename to inst/rmarkdown/templates/rnaseq/skeleton/skeleton.Rmd
diff --git a/inst/rmarkdown/templates/rnaseqv2/template.yaml b/inst/rmarkdown/templates/rnaseq/template.yaml
similarity index 100%
rename from inst/rmarkdown/templates/rnaseqv2/template.yaml
rename to inst/rmarkdown/templates/rnaseq/template.yaml
diff --git a/inst/rmarkdown/templates/rnaseqv2/skeleton/QC/placeholder b/inst/rmarkdown/templates/rnaseqv2/skeleton/QC/placeholder
deleted file mode 100644
index e69de29..0000000