From c0cee02d6e4d13507795fcad6d2a1730d17d8197 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 13 Sep 2023 12:06:36 -0400
Subject: [PATCH] ci: use CI to build cruise & run stubs

---
 .github/workflows/build.yml | 35 +++++++++++++++++++++++++++++++++++
 conf/ci_stub.config         |  8 ++++----
 2 files changed, 39 insertions(+), 4 deletions(-)
 create mode 100644 .github/workflows/build.yml

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
new file mode 100644
index 0000000..738e995
--- /dev/null
+++ b/.github/workflows/build.yml
@@ -0,0 +1,35 @@
+name: build
+
+on:
+  push:
+    branches:
+      - main
+      - develop
+  pull_request:
+    branches:
+      - main
+      - develop
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: "pip"
+      - name: Install nextflow
+        uses: nf-core/setup-nextflow@v1
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip setuptools
+          pip install .[dev,test]
+      - name: Test stub run
+        run: |
+          cruise run -profile ci_stub -stub
diff --git a/conf/ci_stub.config b/conf/ci_stub.config
index 7a2cb18..0729e93 100644
--- a/conf/ci_stub.config
+++ b/conf/ci_stub.config
@@ -1,10 +1,10 @@
 params {
-    config_profile_name = 'Test stubs'
-    config_profile_description = 'Minimal test dataset for continuous integration'
+    config_profile_name = 'Test single-end stubs'
+    config_profile_description = 'Minimal test dataset with blank references to run stubs with continuous integration'
 
     outdir = 'results/test'
-    input = null
-    genome = null
+    input = 'assets/samplesheet_test.csv' // adapted from https://github.com/nf-core/test-datasets/blob/chipseq/samplesheet/v2.0/samplesheet_test.csv
+    genome = 'test'
 
     max_cpus = 2        // for GitHub Actions https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
     max_memory = '6.GB'