From ce0db16615336546d6683f5ec4da36b0b2316edb Mon Sep 17 00:00:00 2001
From: Felipe Marques de Almeida <felipemarques89@gmail.com>
Date: Tue, 13 Feb 2024 11:15:15 +0000
Subject: [PATCH] update ci.yml for nf-test

---
 .github/workflows/ci.yml | 68 +++++++++++++++++++++++++++++-----------
 1 file changed, 49 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e8907caf..574c5fd3 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,39 +1,43 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.1"
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  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/scrnaseq') }}"
+    name: ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
+    needs: [changes, define_nxf_versions]
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        profile: [
-            "test,docker --aligner alevin",
-            "test,docker --aligner kallisto",
-            "test,docker --aligner star",
-            "test,docker --aligner cellranger",
-            # "test,docker --aligner cellrangerarc", // this currently lacks a suitable test profile, see issue https://github.com/nf-core/scrnaseq/issues/290
-            # "test,docker --aligner universc", // this is broken, see issue https://github.com/nf-core/scrnaseq/issues/289
+        profile:
+          [
+            "tests/main_pipeline_alevin.test",
+            "tests/main_pipeline_cellranger.test",
+            "tests/main_pipeline_kallisto.test",
+            "tests/main_pipeline_star.test",
           ]
+
     steps:
       - name: Free some space
         run: |
@@ -41,6 +45,7 @@ jobs:
           sudo rm -rf /opt/ghc
           sudo rm -rf "/usr/local/share/boost"
           sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
       - name: Check out pipeline code
         uses: actions/checkout@v4
 
@@ -49,8 +54,33 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run pipeline with test data
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: Run nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }} --outdir ./results
+          nf-test test "${{ matrix.profile }}" --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml