Feature/run locally

.Rbuildignore

@@ -6,7 +6,14 @@ environment.yml
 run_pipeline.sh
 scripts
 snakemake
-tests
 venv
 .idea
-.env_example
+.env_example
+.env
+.cache
+^\.github$
+^\.lintr$
+^PLATFORM_SETUP\.md$
+^\.git$
+^\.gitignore$
+^\.cursorrules$

.dockerignore

@@ -0,0 +1,29 @@
+.git
+.github
+.cursorrules
+.snakemake
+.genehackman
+.cache
+pipeline_logs
+.ipynb_checkpoints
+.env
+.env_example
+*.sif
+build
+build.log
+README.pdf
+tests/testthat/data
+venv
+__pycache__
+*.pyc
+.pytest_cache
+.quarto
+**/*.quarto_ipynb
+*input.yaml
+*input.json
+.Rproj.user
+.DS_Store
+ieugwasr_oauth
+PLATFORM_SETUP.md
+extract_by_range.r
+input_for_project.yaml

.env_example

@@ -1,8 +1,10 @@
-DATA_DIR=
-RESULTS_DIR=
-RDFS_DIR=
-GENOMIC_DATA_DIR=/mnt/storage/private/mrcieu/data/genomic_data/
-THOUSAND_GENOMES_DIR=/mnt/storage/private/mrcieu/data/genomic_data/1000genomes/b37_dbsnp156/
-LDSC_DIR=/mnt/storage/private/mrcieu/data/LDSCORE/b37_dbsnp156/
-QTL_DIRECTORY=/mnt/storage/private/mrcieu/data/qtl_datasets/
-DOCKER_VERSION=
+#Mandatory variables
+PIPELINE_DATA_DIR=
+PROJECT_DIR=
+DOCKER_VERSION=1.1.0
+# Optional variables
+QTL_DATA_DIR=
+SNAKEMAKE_PROFILE=snakemake/profiles/local/
+APPTAINER_MODULE=
+SLURM_PARTITION=
+SLURM_ACCOUNT=

.github/workflows/main.yml

@@ -0,0 +1,37 @@
+name: CI/CD
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    types: [opened, reopened, ready_for_review, synchronize]
+
+jobs:
+  devtools_check:
+    runs-on: ubuntu-latest
+    container:
+      image: mrcieu/genehackman:develop
+      env:
+        R_LIBS_SITE: /usr/lib/R/site-library
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Run devtools::check()
+        run: Rscript -e "devtools::check()"
+  end_to_end_tests_run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Check that end-to-end tests have been run successfully
+        env:
+          BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+        run: |
+          if [ ! -f tests/testing_complete.txt ]; then
+            echo "Tests have not been run successfully, please run ./tests/e2e_tests/run_test_pipelines.sh and commit the results"
+            exit 1
+          fi
+          if [ "$BRANCH_NAME" != "main" ] && ! grep -q "$BRANCH_NAME" tests/testing_complete.txt; then
+            echo "Tests have not been run successfully for branch: $BRANCH_NAME, please run Rscript tests/testthat/run_tests.R and commit the results"
+            exit 1
+          fi

.gitignore

@@ -1,9 +1,17 @@
 .Rproj.user
+.cursorrules
 .snakemake/
+.genehackman/
+pipeline_logs/
 .cache/
 .ipynb_checkpoints/
+*input.yaml
 *input.json
 .env
 .bashrc
 .DS_Store
 ieugwasr_oauth
+__pycache__/
+
+/.quarto/
+**/*.quarto_ipynb

.lintr

@@ -0,0 +1,5 @@
+linters: with_defaults(
+  line_length_linter = line_length_linter(120),
+  quotes_linter = NULL,
+  object_name_linter = NULL
+)