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: ${{ runner.os }}
diff --git a/R/melt_finemapping_results.R b/R/melt_finemapping_results.R
deleted file mode 100644
index 2ccb9cb..0000000
--- a/R/melt_finemapping_results.R
+++ /dev/null
@@ -1,25 +0,0 @@
-melt_finemapping_results <- function(dat,
- verbose = TRUE) {
- PP_cols <- grep("\\.PP$", colnames(dat), value = TRUE)
- CS_cols <- grep("\\.CS$", colnames(dat), value = TRUE)
- messager("Melting PP and CS from", length(CS_cols), "fine-mapping methods",
- v = verbose
- )
- finemap_melt <- suppressWarnings(
- data.table::melt.data.table(data.table::data.table(dat),
- measure.vars = list(PP_cols, CS_cols),
- variable.name = "Method",
- variable.factor = TRUE,
- value.name = c("PP", "CS")
- )
- )
- methods_key <- setNames(
- gsub("\\.PP", "", PP_cols),
- unique(finemap_melt$Method)
- )
- finemap_melt$Method <- factor(methods_key[finemap_melt$Method],
- levels = unname(methods_key),
- ordered = TRUE
- )
- return(finemap_melt)
-}
diff --git a/README.Rmd b/README.Rmd
index 1f70953..689cd32 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -1,12 +1,6 @@
---
title: ""
-author: "
- `r badger::badge_github_version(color = 'black')`
- `r badger::badge_github_actions(action = 'rworkflows')`
- `r badger::badge_last_commit(branch = 'main')`
- `r badger::badge_codecov(branch = 'main')`
- `r badger::badge_license()`
-