From 1e8a8cdd17c03a2352b91a51f664ff78ec3a2633 Mon Sep 17 00:00:00 2001
From: Joon-Klaps <joon.klaps@gmail.com>
Date: Thu, 28 Sep 2023 16:53:53 +0200
Subject: [PATCH] add ci tests

---
 .github/workflows/{ci.yml => ci_test.yml} |  4 +--
 .github/workflows/ci_test_full.yml        | 40 +++++++++++++++++++++++
 .github/workflows/ci_test_umi.yml         | 40 +++++++++++++++++++++++
 3 files changed, 82 insertions(+), 2 deletions(-)
 rename .github/workflows/{ci.yml => ci_test.yml} (92%)
 create mode 100644 .github/workflows/ci_test_full.yml
 create mode 100644 .github/workflows/ci_test_umi.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci_test.yml
similarity index 92%
rename from .github/workflows/ci.yml
rename to .github/workflows/ci_test.yml
index 75549c32..666aeb3a 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci_test.yml
@@ -35,9 +35,9 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
+      - name: Run pipeline with small test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --max_cpus 2 --max_memory 4GB
diff --git a/.github/workflows/ci_test_full.yml b/.github/workflows/ci_test_full.yml
new file mode 100644
index 00000000..cd4e5d95
--- /dev/null
+++ b/.github/workflows/ci_test_full.yml
@@ -0,0 +1,40 @@
+name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+env:
+  NXF_ANSI_LOG: false
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Run pipeline with test data
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Run pipeline with complete test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_full,docker --outdir ./results --max_cpus 2 --max_memory 4GB
diff --git a/.github/workflows/ci_test_umi.yml b/.github/workflows/ci_test_umi.yml
new file mode 100644
index 00000000..09d630a1
--- /dev/null
+++ b/.github/workflows/ci_test_umi.yml
@@ -0,0 +1,40 @@
+name: nf-core CI
+# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+on:
+  push:
+    branches:
+      - dev
+  pull_request:
+  release:
+    types: [published]
+
+env:
+  NXF_ANSI_LOG: false
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Run pipeline with test data
+    # Only run on push if this is the nf-core dev branch (merged PRs)
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/viralgenie') }}"
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
+    steps:
+      - name: Check out pipeline code
+        uses: actions/checkout@v3
+
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Run pipeline with umi test data
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test_umi,docker --outdir ./results --max_cpus 2 --max_memory 4GB