From ac3680e9171d0e64e17cd9fd297c1d5df30b6dc3 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 1 May 2024 10:08:39 +0100
Subject: [PATCH 1/8] Copy in CI from fetchngs

---
 .github/workflows/ci.yml | 77 ++++++++++++++++++++++++++--------------
 1 file changed, 50 insertions(+), 27 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index faa0742..3b1c9c6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,18 +1,22 @@
-name: nf-aggregate 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:
   pull_request:
   release:
-    types:
-      - published
+    types: [published]
   merge_group:
     types:
       - checks_requested
     branches:
       - master
+      - dev
 
 env:
   NXF_ANSI_LOG: false
+  NFT_VER: "0.8.4"
+  NFT_WORKDIR: "~"
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
@@ -20,49 +24,61 @@ concurrency:
 
 jobs:
   changes:
-    name: Find tags to test
+    name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      tags: ${{ steps.get_tags.outputs.result }}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
       - uses: actions/checkout@v3
-      - name: Combine all tags.yml files
-        id: get_username
-        run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml
-      - name: debug
-        run: cat .github/tags.yml
-      - name: Get tags using yq
-        id: get_tags
-        uses: mikefarah/yq@master
         with:
-          cmd: yq -e '. | keys | tojson' .github/tags.yml
+          fetch-depth: 0
+
+      - name: List nf-test files
+        id: list
+        uses: adamrtalbot/detect-nf-test-changes@v0.0.3
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
 
-  nf-test:
-    name: nf-test ${{ matrix.tags }} ${{ matrix.profile }} nf-${{ matrix.NXF_VER }}
+      - name: print list of nf-test files
+        run: |
+          echo ${{ steps.list.outputs.components }}
+
+  test:
+    name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
     needs: [changes]
-    if: needs.changes.outputs.tags != '[]'
+    if: needs.changes.outputs.nf_test_files != '[]'
     runs-on: ubuntu-latest
-    env:
-      TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
     strategy:
       fail-fast: false
       matrix:
         NXF_VER:
-          - "23.10.0"
           - "latest-everything"
-        tags: ${{ fromJson(needs.changes.outputs.tags) }}
+          - "23.04"
+        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+          architecture: "x64"
+
+      - name: Install pdiff to see diff between nf-test snapshots
+        run: |
+          python -m pip install --upgrade pip
+          pip install pdiff
+
       - name: Cache nf-test installation
         id: cache-software
         uses: actions/cache@v3
@@ -70,7 +86,7 @@ jobs:
           path: |
             /usr/local/bin/nf-test
             /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+          key: ${{ runner.os }}-${{ env.NFT_VER }}-nftest
 
       - name: Install nf-test
         if: steps.cache-software.outputs.cache-hit != 'true'
@@ -80,7 +96,12 @@ jobs:
 
       - name: Run nf-test
         run: |
-          nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml --verbose
+          nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap
+
+      - uses: pcolby/tap-summary@v1
+        with:
+          path: >-
+            test.tap
 
       - name: Output log on failure
         if: failure()
@@ -96,11 +117,13 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [changes, nf-test]
+    needs:
+      - changes
+      - test
     if: always()
     steps:
       - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
+        if: ${{ !contains(needs.*.result, 'failure') }}
         run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}

From ee757cf6cf930c6179fb6cf5d22b5f2d2dce61bc Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 1 May 2024 10:11:40 +0100
Subject: [PATCH 2/8] Add include.yaml

---
 .github/include.yaml | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 .github/include.yaml

diff --git a/.github/include.yaml b/.github/include.yaml
new file mode 100644
index 0000000..a3629f4
--- /dev/null
+++ b/.github/include.yaml
@@ -0,0 +1,10 @@
+".":
+  - ./.github/workflows/**
+  - ./nf-test.config
+  - ./nextflow.config
+tests:
+  - ./assets/*
+  - ./bin/*
+  - ./conf/*
+  - ./main.nf
+  - ./nextflow_schema.json

From dbcc41e960c06484b9f0d440f86295005ca54210 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Wed, 1 May 2024 10:23:31 +0100
Subject: [PATCH 3/8] Bump tower-cli

---
 modules/local/seqera_runs_dump/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/seqera_runs_dump/main.nf b/modules/local/seqera_runs_dump/main.nf
index 1628beb..9a69300 100644
--- a/modules/local/seqera_runs_dump/main.nf
+++ b/modules/local/seqera_runs_dump/main.nf
@@ -2,8 +2,8 @@ include { getRunMetadata } from './functions'
 
 process SEQERA_RUNS_DUMP {
     tag "$meta.id"
-    conda 'tower-cli=0.9.0'
-    container 'seqeralabs/nf-aggregate:tower-cli-0.9.0--2cb0f2e9d85d026b'
+    conda 'tower-cli=0.9.2'
+    container 'seqeralabs/nf-aggregate:tower-cli-0.9.2--hdfd78af_1'
 
     input:
     val meta

From 0389e614cd688dac1c156d0fc8b0420583c42090 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 3 May 2024 08:23:18 +0000
Subject: [PATCH 4/8] Older nf won't work

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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3b1c9c6..ce46484 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -55,7 +55,6 @@ jobs:
       matrix:
         NXF_VER:
           - "latest-everything"
-          - "23.04"
         nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
         profile:
           - "docker"

From 9111f97b60c82876a8d5d602f24fa14dc71cbfcf Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 3 May 2024 08:36:25 +0000
Subject: [PATCH 5/8] Fix up tests for utils_nf_aggregate

---
 subworkflows/local/utils_nf_aggregate/tests/main.nf.test | 6 ++++--
 workflows/nf_aggregate/tests/main.nf.test.snap           | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
index ecc46f5..f4777de 100644
--- a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
+++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
@@ -9,16 +9,18 @@ nextflow_workflow {
     
     stage {
         symlink "nextflow_schema.json"
-        symlink "workflows/nf_aggregate/assets/test_run_ids.csv"
     }
 
     test("Should run without failures") {
 
         when {
+            params {
+                input = "${projectDir}/workflows/nf_aggregate/assets/test_run_ids.csv"
+            }
             workflow {
                 """
                 // define inputs of the workflow here. Example:
-                // input[0] = file("test-file.txt")
+                // input[0] = file("test_run_ids.csv")
                 """
             }
         }
diff --git a/workflows/nf_aggregate/tests/main.nf.test.snap b/workflows/nf_aggregate/tests/main.nf.test.snap
index 6baffb1..3709bad 100644
--- a/workflows/nf_aggregate/tests/main.nf.test.snap
+++ b/workflows/nf_aggregate/tests/main.nf.test.snap
@@ -10,6 +10,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-02T13:45:38.806631609"
+        "timestamp": "2024-05-03T08:19:43.740440752"
     }
 }
\ No newline at end of file

From 946bffdd5127d61fd808d3dc6c10d6e9d0042fb7 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 3 May 2024 08:50:57 +0000
Subject: [PATCH 6/8] Revert "Fix up tests for utils_nf_aggregate"

This reverts commit 9111f97b60c82876a8d5d602f24fa14dc71cbfcf.
---
 subworkflows/local/utils_nf_aggregate/tests/main.nf.test | 6 ++----
 workflows/nf_aggregate/tests/main.nf.test.snap           | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
index f4777de..ecc46f5 100644
--- a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
+++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test
@@ -9,18 +9,16 @@ nextflow_workflow {
     
     stage {
         symlink "nextflow_schema.json"
+        symlink "workflows/nf_aggregate/assets/test_run_ids.csv"
     }
 
     test("Should run without failures") {
 
         when {
-            params {
-                input = "${projectDir}/workflows/nf_aggregate/assets/test_run_ids.csv"
-            }
             workflow {
                 """
                 // define inputs of the workflow here. Example:
-                // input[0] = file("test_run_ids.csv")
+                // input[0] = file("test-file.txt")
                 """
             }
         }
diff --git a/workflows/nf_aggregate/tests/main.nf.test.snap b/workflows/nf_aggregate/tests/main.nf.test.snap
index 3709bad..6baffb1 100644
--- a/workflows/nf_aggregate/tests/main.nf.test.snap
+++ b/workflows/nf_aggregate/tests/main.nf.test.snap
@@ -10,6 +10,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-03T08:19:43.740440752"
+        "timestamp": "2024-05-02T13:45:38.806631609"
     }
 }
\ No newline at end of file

From 8de332df68aea8a5842b3c98a41adfb2783f5455 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 3 May 2024 08:51:56 +0000
Subject: [PATCH 7/8] Activate test profile for nf-test

---
 nf-test.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nf-test.config b/nf-test.config
index c7fed01..97ad11b 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -9,5 +9,5 @@ config {
     configFile "tests/nextflow.config"
 
     // run all test with the defined docker profile from the main nextflow.config
-    profile ""
+    profile "test"
 }

From deebe24d98704fcc6b250a54698dcde415ecad45 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Fri, 3 May 2024 08:57:38 +0000
Subject: [PATCH 8/8] Add token to env

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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index ce46484..78f57e6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -17,6 +17,7 @@ env:
   NFT_WORKDIR: "~"
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
+  TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"