From 356667ea9a13dd11e0a35aa07797e51b88731f67 Mon Sep 17 00:00:00 2001
From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com>
Date: Wed, 2 Oct 2024 20:34:06 +0100
Subject: [PATCH] fix GH token in GHA

---
 .github/workflows/rworkflows.yml | 2 +-
 R/check_peakfiles.R              | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 R/check_peakfiles.R

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 8a656cf..cb22370 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -41,7 +41,7 @@ jobs:
         run_covr: ${{ true }}
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
-        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ true }}
         docker_user: bschilder
         docker_org: neurogenomicslab
diff --git a/R/check_peakfiles.R b/R/check_peakfiles.R
new file mode 100644
index 0000000..40bc094
--- /dev/null
+++ b/R/check_peakfiles.R
@@ -0,0 +1,5 @@
+check_peakfiles <- function(peakfiles){
+  if(all(unlist(lapply(peakfiles,length))==0)){
+    stopper("No peaks found in any of the peakfiles.")
+  }
+}
\ No newline at end of file