From 132017893f7c3a11b39c151883cf964961f9b63a Mon Sep 17 00:00:00 2001
From: "Brian M. Schilder" <34280215+bschilder@users.noreply.github.com>
Date: Fri, 27 Oct 2023 12:45:09 +0100
Subject: [PATCH] Use dev version of rworkflows

---
 .DS_Store                        | Bin 0 -> 8196 bytes
 .github/.DS_Store                | Bin 0 -> 6148 bytes
 .github/workflows/rworkflows.yml |   7 +++++--
 vignettes/MungeSumstats.Rmd      |   2 +-
 4 files changed, 6 insertions(+), 3 deletions(-)
 create mode 100644 .DS_Store
 create mode 100644 .github/.DS_Store

diff --git a/.DS_Store b/.DS_Store
new file mode 100644
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GIT binary patch
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diff --git a/.github/.DS_Store b/.github/.DS_Store
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GIT binary patch
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diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 8f0801c..01a8e44 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -4,14 +4,17 @@ name: rworkflows
     branches:
     - master
     - main
+    - devel
     - RELEASE_**
   pull_request:
     branches:
     - master
     - main
+    - devel
     - RELEASE_**
 jobs:
   rworkflows:
+    permissions: write-all
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -31,7 +34,7 @@ jobs:
         #   r: latest
         #   bioc: release
     steps:
-    - uses: neurogenomics/rworkflows@master
+    - uses: neurogenomics/rworkflows@dev
       with:
         run_bioccheck: ${{ true }}
         run_rcmdcheck: ${{ true }}
@@ -42,7 +45,7 @@ jobs:
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
         has_latex: ${{ false }}
-        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ true }}
         docker_user: almurphy
         docker_org: neurogenomicslab
diff --git a/vignettes/MungeSumstats.Rmd b/vignettes/MungeSumstats.Rmd
index 3a2ad60..089e745 100644
--- a/vignettes/MungeSumstats.Rmd
+++ b/vignettes/MungeSumstats.Rmd
@@ -659,7 +659,7 @@ To do this, simply run the following:
 ```{r}
 eduAttainOkbayPth <- system.file("extdata", "eduAttainOkbay.txt",
                                   package = "MungeSumstats")
-formatted_path <- tempfile(fileext = "eduAttainOkbay_standardised.tsv.gz")
+formatted_path <- tempfile(fileext = "_eduAttainOkbay_standardised.tsv.gz")
 
 
 #### 1. Read in the data and standardise header names ####