From 8e79d5ca70e26b5bdf524a9d33515488a0c7e2ce Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 4 Oct 2023 20:50:14 -0500
Subject: [PATCH 1/4] ci: Write initial scatter CI

---
 .github/workflows/ci.yml | 30 ++++++++++++++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 439bd09c..f2014d42 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -16,10 +16,35 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  list:
+    name: List Tests
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nascent') }}"
+    outputs:
+      # Expose matched filters as job 'modules' output variable
+      tests: ${{ steps.list.outputs.tests }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Setup Nextflow
+        uses: nf-core/setup-nextflow@v1
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
+
+      - name: List nf-test
+        id: list
+        run: |
+          echo "tests=$(nf-test list --silent --format=json)" >> "$GITHUB_OUTPUT"
+
   test:
     name: nf-test ${{ matrix.profile }}-${{ matrix.NXF_VER }}
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nascent') }}"
+    if: needs.list.outputs.tests != '[]'
+    needs: [list]
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -27,6 +52,7 @@ jobs:
           - "23.04.0"
           - "latest-everything"
         profile: ["docker"] # TODO , "singularity", "conda"]
+        test: ["${{ fromJson(needs.list.outputs.tests) }}"]
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -73,7 +99,7 @@ jobs:
         run: |
           nf-test test \
             --profile=${{ matrix.profile }} \
-            tests/pipeline/*.nf.test \
+            ${{ matrix.test }} \
             --tap=test.tap
 
       - uses: pcolby/tap-summary@v1

From b696e773f342dd0e4f11a987ecb2ce48727962e4 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 4 Oct 2023 22:36:50 -0500
Subject: [PATCH 2/4] ci: Add test report workflow

---
 .github/workflows/ci.yml          | 10 +++++-----
 .github/workflows/test-report.yml | 20 ++++++++++++++++++++
 2 files changed, 25 insertions(+), 5 deletions(-)
 create mode 100644 .github/workflows/test-report.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f2014d42..e468b362 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -100,9 +100,9 @@ jobs:
           nf-test test \
             --profile=${{ matrix.profile }} \
             ${{ matrix.test }} \
-            --tap=test.tap
-
-      - uses: pcolby/tap-summary@v1
+            --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml
+      - uses: actions/upload-artifact@v3 # upload test results
+        if: success() || failure() # run this step even if previous step failed
         with:
-          path: >-
-            test.tap
+          name: test-results
+          path: ${{ matrix.test }}-${{ matrix.profile }}.xml
diff --git a/.github/workflows/test-report.yml b/.github/workflows/test-report.yml
new file mode 100644
index 00000000..cee35a59
--- /dev/null
+++ b/.github/workflows/test-report.yml
@@ -0,0 +1,20 @@
+name: "Test Report"
+on:
+  workflow_run:
+    workflows: ["nf-core CI"] # runs after CI workflow
+    types:
+      - completed
+permissions:
+  contents: read
+  actions: read
+  checks: write
+jobs:
+  report:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: dorny/test-reporter@v1
+        with:
+          artifact: test-results # artifact name
+          name: JEST Tests # Name of the check run which will be created
+          path: "*.xml" # Path to test results (inside artifact .zip)
+          reporter: jest-junit # Format of test results

From dcfbf52eb971bb5312992ce1b82cf8648cc6d901 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 4 Oct 2023 22:48:41 -0500
Subject: [PATCH 3/4] ci: Add test profile

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e468b362..885509c0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -98,7 +98,7 @@ jobs:
       - name: Run nf-test
         run: |
           nf-test test \
-            --profile=${{ matrix.profile }} \
+            --profile="test,${{ matrix.profile }}" \
             ${{ matrix.test }} \
             --junitxml=${{ matrix.test }}-${{ matrix.profile }}.xml
       - uses: actions/upload-artifact@v3 # upload test results

From 7532677565d2f4f03ddf5796029cc1d3ae4953e4 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.a.miller@protonmail.com>
Date: Wed, 4 Oct 2023 23:03:10 -0500
Subject: [PATCH 4/4] ci: Ignore grohmm tests

---
 .github/workflows/ci.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 885509c0..3dd86b38 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -53,6 +53,10 @@ jobs:
           - "latest-everything"
         profile: ["docker"] # TODO , "singularity", "conda"]
         test: ["${{ fromJson(needs.list.outputs.tests) }}"]
+        exclude:
+          - test: "tests/subworkflows/local/grohmm/main.nf.test@3508b8c9"
+          - test: "tests/subworkflows/local/grohmm/main.nf.test@716555be"
+          - test: "tests/subworkflows/local/grohmm/main.nf.test@306b4b15"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3