diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ee5ae5a..a157623 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,7 +1,7 @@ name: Continuous Integration on: - pull_request_target: + pull_request: paths-ignore: - .github/* - .gitignore @@ -46,39 +46,6 @@ jobs: - name: Check unit test code coverage run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml codecov - ci_osx-64: - name: osx-64 CI - runs-on: macos-13 - strategy: - fail-fast: false - matrix: - environment: ["r43", "r44"] - - steps: - - name: Checkout pull request branch - uses: actions/checkout@v5 - with: - fetch-depth: 0 - - - name: Create TOML from recipe - run: | - .github/workflows/create_toml_from_yaml.sh ${GITHUB_WORKSPACE} - mkdir /tmp/pixi - mv ${GITHUB_WORKSPACE}/pixi.toml /tmp/pixi - - - name: Setup pixi - uses: prefix-dev/setup-pixi@v0.9.2 - with: - manifest-path: /tmp/pixi/pixi.toml - - - name: Run unit tests - run: pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml devtools_test - - - name: Run R CMD CHECK - run: | - pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml build - pixi run --environment ${{ matrix.environment }} --manifest-path /tmp/pixi/pixi.toml rcmdcheck - ci_osx-arm64: name: osx-arm64 CI runs-on: macos-14 diff --git a/vignettes/ColocBoost_Wrapper_Pipeline.Rmd b/vignettes/ColocBoost_Wrapper_Pipeline.Rmd index 6b5a5a4..ebe9da1 100644 --- a/vignettes/ColocBoost_Wrapper_Pipeline.Rmd +++ b/vignettes/ColocBoost_Wrapper_Pipeline.Rmd @@ -63,7 +63,7 @@ outputs: The following example demonstrates how to set up input data with 3 phenotypes and 2 cohorts. The first cohort has 2 phenotypes and the second cohort has 1 phenotype. The first phenotype has 2 genes and the second phenotype has 1 gene. -```{r, data-loader-individual} +```{r, data-loader-individual, eval = FALSE} # Example of loading individual-level data region = "chr1:1000000-2000000" genotype_list = c("plink_cohort1.1", "plink_cohort1.2") @@ -127,7 +127,7 @@ outputs: The following example demonstrates how to set up input data with 2 summary statistics and one LD reference. -```{r, data-loader-sumstat} +```{r, data-loader-sumstat, eval = FALSE} # Example of loading summary statistics sumstat_path_list = c("sumstat1.tsv.gz", "sumstat2.tsv.gz") column_file_path_list = c("column_mapping_sumstat1.yml", "column_mapping_sumstat2.yml") @@ -222,7 +222,7 @@ Example: for sQTL, `list(type_pattern = ".*clu_(\\d+_[+-?]).*", valid_pattern = outputs: - **`colocboost_results`**: List of colocboost objects (with `xqtl_coloc`, `joint_gwas`, `separate_gwas`); Output of the `colocboost_analysis_pipeline` function. If the mode is not run, the corresponding element will be `NULL`. -```{r, colocboost-analysis} +```{r, colocboost-analysis, eval = FALSE} # load in individual-level and sumstat data region_data_combined <- load_multitask_regional_data( region = region, @@ -277,4 +277,4 @@ colocboost_plot(colocboost_results$joint_gwas) for (i in 1:length(colocboost_results$separate_gwas)) { colocboost_plot(colocboost_results$separate_gwas[[i]]) } -``` \ No newline at end of file +```