diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index 3d71631..9b40bf2 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -4,14 +4,19 @@ name: rworkflows
branches:
- master
- main
+ - devel
- RELEASE_**
pull_request:
branches:
- master
- main
+ - devel
- RELEASE_**
jobs:
rworkflows:
+ permissions:
+ contents: write
+ packages: write
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
@@ -20,16 +25,20 @@ jobs:
matrix:
config:
- os: ubuntu-latest
- r: devel
bioc: devel
- cont: bioconductor/bioconductor_docker:devel
- rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release
+ r: auto
+ cont: ghcr.io/bioconductor/bioconductor_docker:devel
+ rspm: https://packagemanager.rstudio.com/cran/__linux__/latest/release
- os: macOS-latest
- r: latest
bioc: release
+ r: auto
+ cont: ~
+ rspm: ~
- os: windows-latest
- r: latest
bioc: release
+ r: auto
+ cont: ~
+ rspm: ~
steps:
- uses: neurogenomics/rworkflows@master
with:
@@ -42,7 +51,7 @@ jobs:
run_pkgdown: ${{ true }}
has_runit: ${{ false }}
has_latex: ${{ false }}
- GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run_docker: ${{ false }}
DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
runner_os: ${{ runner.os }}
diff --git a/README.Rmd b/README.Rmd
index f8e5d5d..698240e 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -7,12 +7,14 @@ output:
```{r, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
-description <- read.dcf("DESCRIPTION", fields = "Description")[1]
+description <- read.dcf("DESCRIPTION", fields = "Description")[1] |>
+ gsub(pattern="\n", replacement=" ")
```
## ``r pkg``: `r gsub("echoverse module: ","", description)`
-This R package is part of the *echoverse* suite that supports [`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
+This R package is part of the *echoverse* suite that supports
+[`echolocatoR`](https://github.com/RajLabMSSM/echolocatoR):
an automated genomic fine-mapping pipeline.
If you use ``r pkg``, please cite:
diff --git a/README.md b/README.md
index bfef821..5decfa5 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@ GPL-3](https://img.shields.io/badge/license-GPL--3-blue.svg)](https://cran.r-pro
[![](https://img.shields.io/github/last-commit/RajLabMSSM/echoverseTemplate.svg)](https://github.com/RajLabMSSM/echoverseTemplate/commits/master)
[![R build
status](https://github.com/RajLabMSSM/echoverseTemplate/workflows/rworkflows/badge.svg)](https://github.com/RajLabMSSM/echoverseTemplate/actions)
-[![](https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graph/badge.svg)](https://codecov.io/gh/RajLabMSSM/echoverseTemplate)
+[![](https://codecov.io/gh/RajLabMSSM/echoverseTemplate/branch/master/graph/badge.svg)](https://app.codecov.io/gh/RajLabMSSM/echoverseTemplate)