From 968230547794854cf772b5aba2eee4caefaea976 Mon Sep 17 00:00:00 2001
From: js2264 <jacquesserizay@gmail.com>
Date: Fri, 26 Jul 2024 00:06:33 +0200
Subject: [PATCH] fix: switch to js2264/rworkflows to see if quarto rendering
 works

---
 .github/workflows/rworkflows.yml |  2 +-
 vignettes/manuscript_figure.qmd  | 12 ++++++++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 94d43eb..9266ad0 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -38,7 +38,7 @@ jobs:
           cont: ~
           rspm: ~
     steps:
-    - uses: neurogenomics/rworkflows@master
+    - uses: js2264/rworkflows@master
       with:
         run_bioccheck: ${{ false }}
         run_rcmdcheck: ${{ true }}
diff --git a/vignettes/manuscript_figure.qmd b/vignettes/manuscript_figure.qmd
index c53a986..a3d9469 100644
--- a/vignettes/manuscript_figure.qmd
+++ b/vignettes/manuscript_figure.qmd
@@ -10,11 +10,19 @@ knitr::opts_chunk$set(
     width = 180, 
     error = TRUE
 )
+library(tidyCoverage)
+library(AnnotationHub)
+library(purrr)
+library(plyranges)
+library(rtracklayer)
+library(ggplot2) 
 ```
 
 # Plotting aggregate signals (ENCODE data) over REs
 
-```{r}
+_Note: this is a Quarto vignette (`.qmd`)_
+
+```{r, eval = FALSE}
 library(tidyCoverage)
 library(AnnotationHub)
 library(purrr)
@@ -92,7 +100,7 @@ AC |>
 
 # Plotting matrix signals (ENCODE data) over REs
 
-```{r}
+```{r, eval = FALSE}
 expand(CE) |> 
     filter(track == "ATAC") |> 
     select(-coord) |>