From e519b3ff1b99b9fbbfc41adab0566e2a461fc0a7 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 27 Feb 2025 11:22:11 +0100
Subject: [PATCH 1/6] nf-test sharding

---
 .github/actions/get-shards/action.yml         |  66 +++++++++
 .github/actions/nf-test/action.yml            |  97 +++++++++++++
 .github/workflows/ci.yml                      | 136 ------------------
 .github/workflows/nf-test.yml                 | 131 +++++++++++++++++
 .../local/utils_nf_aggregate/tests/tags.yml   |   2 -
 workflows/nf_aggregate/tests/tags.yml         |   2 -
 6 files changed, 294 insertions(+), 140 deletions(-)
 create mode 100644 .github/actions/get-shards/action.yml
 create mode 100644 .github/actions/nf-test/action.yml
 delete mode 100644 .github/workflows/ci.yml
 create mode 100644 .github/workflows/nf-test.yml
 delete mode 100644 subworkflows/local/utils_nf_aggregate/tests/tags.yml
 delete mode 100644 workflows/nf_aggregate/tests/tags.yml

diff --git a/.github/actions/get-shards/action.yml b/.github/actions/get-shards/action.yml
new file mode 100644
index 0000000..52356bf
--- /dev/null
+++ b/.github/actions/get-shards/action.yml
@@ -0,0 +1,66 @@
+name: "Get number of shards"
+description: "Get the number of nf-test shards for the current CI job"
+inputs:
+  max_shards:
+    description: "Maximum number of shards allowed"
+    required: true
+  paths:
+    description: "Component paths to test"
+    required: false
+outputs:
+  shard:
+    description: "Array of shard numbers"
+    value: ${{ steps.shards.outputs.shard }}
+  total_shards:
+    description: "Total number of shards"
+    value: ${{ steps.shards.outputs.total_shards }}
+runs:
+  using: "composite"
+  steps:
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: ${{ env.NFT_VER }}
+    - name: Get number of shards
+      id: shards
+      shell: bash
+      run: |
+        # Run nf-test with dynamic parameter
+        nftest_output=$(nf-test test \
+          --dry-run \
+          --profile +docker \
+          --filter module,function,workflow,pipeline \
+          --ci \
+          --changed-since HEAD^) || {
+            echo "nf-test command failed with exit code $?"
+            echo "Full output: $nftest_output"
+            exit 1
+        }
+        echo "nf-test dry-run output: $nftest_output"
+
+        # Default values for shard and total_shards
+        shard="[]"
+        total_shards=0
+
+        # Check if there are related tests
+        if echo "$nftest_output" | grep -q 'No tests to execute'; then
+          echo "No related tests found."
+        else
+          # Extract the number of related tests
+          number_of_shards=$(echo "$nftest_output" | sed -n 's|.*Executed \([0-9]*\) tests.*|\1|p')
+          if [[ -n "$number_of_shards" && "$number_of_shards" -gt 0 ]]; then
+            shards_to_run=$(( $number_of_shards < ${{ inputs.max_shards }} ? $number_of_shards : ${{ inputs.max_shards }} ))
+            shard=$(seq 1 "$shards_to_run" | jq -R . | jq -c -s .)
+            total_shards="$shards_to_run"
+          else
+            echo "Unexpected output format. Falling back to default values."
+          fi
+        fi
+
+        # Write to GitHub Actions outputs
+        echo "shard=$shard" >> $GITHUB_OUTPUT
+        echo "total_shards=$total_shards" >> $GITHUB_OUTPUT
+
+        # Debugging output
+        echo "Final shard array: $shard"
+        echo "Total number of shards: $total_shards"
diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml
new file mode 100644
index 0000000..fdc8e24
--- /dev/null
+++ b/.github/actions/nf-test/action.yml
@@ -0,0 +1,97 @@
+name: "nf-test Action"
+description: "Runs nf-test with common setup steps"
+inputs:
+  profile:
+    description: "Profile to use"
+    required: true
+  shard:
+    description: "Shard number for this CI job"
+    required: true
+  total_shards:
+    description: "Total number of test shards(NOT the total number of matrix jobs)"
+    required: true
+  paths:
+    description: "Test paths"
+    required: true
+
+runs:
+  using: "composite"
+  steps:
+    - name: Setup Nextflow
+      uses: nf-core/setup-nextflow@v2
+      with:
+        version: "${{ env.NXF_VERSION }}"
+
+    - name: Set up Python
+      uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5
+      with:
+        python-version: "3.11"
+
+    - name: Install nf-test
+      uses: nf-core/setup-nf-test@v1
+      with:
+        version: "${{ env.NFT_VER }}"
+
+    - name: Install pdiff
+      shell: bash
+      run: |
+        python -m pip install pdiff
+
+      # TODO Skip failing conda tests and document their failures
+      # https://github.com/nf-core/modules/issues/7017
+    - name: Run nf-test
+      shell: bash
+      env:
+        NFT_DIFF: ${{ env.NFT_DIFF }}
+        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+        NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+        SENTIEON_AUTH_MECH: "GitHub Actions - token"
+        SENTIEON_LICSRVR_IP: ${{ env.SENTIEON_LICSRVR_IP }}
+      run: |
+        nf-test test \
+          --profile=+${{ inputs.profile }} \
+          --tap=test.tap \
+          --verbose \
+          --ci \
+          --shard ${{ inputs.shard }}/${{ inputs.total_shards }} \
+          --filter module,function,workflow,pipeline
+
+          # Save the absolute path of the test.tap file to the output
+          echo "tap_file_path=$(realpath test.tap)" >> $GITHUB_OUTPUT
+
+    - name: Generate test summary
+      if: always()
+      shell: bash
+      run: |
+        # Add header if it doesn't exist (using a token file to track this)
+        if [ ! -f ".summary_header" ]; then
+          echo "# 🚀 nf-test results" >> $GITHUB_STEP_SUMMARY
+          echo "" >> $GITHUB_STEP_SUMMARY
+          echo "| Status | Test Name | Profile | Shard |" >> $GITHUB_STEP_SUMMARY
+          echo "|:------:|-----------|---------|-------|" >> $GITHUB_STEP_SUMMARY
+          touch .summary_header
+        fi
+
+        if [ -f test.tap ]; then
+          while IFS= read -r line; do
+            if [[ $line =~ ^ok ]]; then
+              test_name="${line#ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ✅ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            elif [[ $line =~ ^not\ ok ]]; then
+              test_name="${line#not ok }"
+              # Remove the test number from the beginning
+              test_name="${test_name#* }"
+              echo "| ❌ | ${test_name} | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+            fi
+          done < test.tap
+        else
+          echo "| ⚠️ | No test results found | ${{ inputs.profile }} | ${{ inputs.shard }}/${{ inputs.total_shards }} |" >> $GITHUB_STEP_SUMMARY
+        fi
+
+    - name: Clean up
+      if: always()
+      shell: bash
+      run: |
+        sudo rm -rf /home/ubuntu/tests/
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
deleted file mode 100644
index 842a9a8..0000000
--- a/.github/workflows/ci.yml
+++ /dev/null
@@ -1,136 +0,0 @@
-# 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]
-  merge_group:
-    types:
-      - checks_requested
-    branches:
-      - master
-      - dev
-
-env:
-  NXF_ANSI_LOG: false
-  NFT_VER: "0.9.2"
-  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 }}"
-  cancel-in-progress: true
-
-jobs:
-  changes:
-    name: Check for changes
-    runs-on: ubuntu-latest
-    outputs:
-      nf_test_files: ${{ steps.list.outputs.components }}
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          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
-
-      - 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.nf_test_files != '[]'
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        NXF_VER:
-          - "latest-everything"
-        nf_test_files: ["${{ fromJson(needs.changes.outputs.nf_test_files) }}"]
-        profile:
-          - "docker"
-
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v4
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
-        with:
-          version: "${{ 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
-        with:
-          path: |
-            /usr/local/bin/nf-test
-            /home/runner/.nf-test/nf-test.jar
-          key: ${{ runner.os }}-${{ env.NFT_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: |
-          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()
-        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
-
-  confirm-pass:
-    runs-on: ubuntu-latest
-    needs:
-      - changes
-      - test
-    if: always()
-    steps:
-      - name: All tests ok
-        if: ${{ !contains(needs.*.result, 'failure') }}
-        run: exit 0
-      - name: One or more tests failed
-        if: ${{ contains(needs.*.result, 'failure') }}
-        run: exit 1
-
-      - name: debug-print
-        if: always()
-        run: |
-          echo "toJSON(needs) = ${{ toJSON(needs) }}"
-          echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
new file mode 100644
index 0000000..6e05b45
--- /dev/null
+++ b/.github/workflows/nf-test.yml
@@ -0,0 +1,131 @@
+name: Run nf-test
+on:
+  push:
+    branches:
+      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
+      - "renovate/**" # branches Renovate creates
+  pull_request:
+    branches: [dev]
+  workflow_dispatch:
+    inputs:
+      runners:
+        description: "Runners to test on"
+        type: choice
+        options:
+          - "ubuntu-latest"
+          - "self-hosted"
+        default: "ubuntu-latest"
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  NFT_DIFF: "pdiff"
+  NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
+  # renovate: datasource=github-releases depName=askimed/nf-test versioning=semver
+  NFT_VER: "0.9.2"
+  NFT_WORKDIR: "~"
+  NXF_ANSI_LOG: false
+  TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
+
+jobs:
+  nf-test-changes:
+    name: nf-test-changes
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    outputs:
+      shard: ${{ steps.set-shards.outputs.shard }}
+      total_shards: ${{ steps.set-shards.outputs.total_shards }}
+    steps:
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: get number of shards
+        id: set-shards
+        uses: ./.github/actions/get-shards
+        env:
+          NFT_VER: ${{ env.NFT_VER }}
+        with:
+          max_shards: 7
+
+      - name: debug
+        run: |
+          echo ${{ steps.set-shards.outputs.shard }}
+          echo ${{ steps.set-shards.outputs.total_shards }}
+
+  nf-test:
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
+    needs: [nf-test-changes]
+    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
+    strategy:
+      fail-fast: false
+      matrix:
+        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
+        profile: [docker]
+        NXF_VER:
+          # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
+          - "24.10.2"
+          - "latest-everything"
+    env:
+      NXF_ANSI_LOG: false
+      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
+
+    steps:
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
+
+      - name: Run nf-test
+        uses: ./.github/actions/nf-test
+        env:
+          NFT_DIFF: ${{ env.NFT_DIFF }}
+          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
+          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
+          TOWER_ACCESS_TOKEN: ${{ env.TOWER_ACCESS_TOKEN }}
+        with:
+          profile: ${{ matrix.profile }}
+          shard: ${{ matrix.shard }}
+          total_shards: ${{ env.TOTAL_SHARDS }}
+
+  confirm-pass:
+    runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
+    needs: [nf-test]
+    if: always()
+    steps:
+      - name: One or more tests failed
+        if: ${{ contains(needs.*.result, 'failure') }}
+        run: exit 1
+
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
+      - name: debug-print
+        if: always()
+        run: |
+          echo "::group::DEBUG: `needs` Contents"
+          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
+          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
+          echo "::endgroup::"
+
+      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
+        if: always()
+        run: |
+          ls -la ./
+          rm -rf ./* || true
+          rm -rf ./.??* || true
+          ls -la ./
diff --git a/subworkflows/local/utils_nf_aggregate/tests/tags.yml b/subworkflows/local/utils_nf_aggregate/tests/tags.yml
deleted file mode 100644
index 4fc1520..0000000
--- a/subworkflows/local/utils_nf_aggregate/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows_local_utils_nf_aggregate:
-  - subworkflows/local/utils_nf_aggregate/**
diff --git a/workflows/nf_aggregate/tests/tags.yml b/workflows/nf_aggregate/tests/tags.yml
deleted file mode 100644
index 50048dc..0000000
--- a/workflows/nf_aggregate/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-workflows_nf_aggregate:
-  - workflows/nf_aggregate/**

From 19a2031d2162f9d7ba38a621cae8d5d38632f487 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 27 Feb 2025 11:25:45 +0100
Subject: [PATCH 2/6] update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index c6df445..298f4fb 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,6 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #74](https://github.com/seqeralabs/nf-aggregate/pull/74) - Add process for generating Benchmark reports
 - [PR #75](https://github.com/seqeralabs/nf-aggregate/pull/75) - Skip failed jobs in benchmarking report
 - [PR #78](https://github.com/seqeralabs/nf-aggregate/pull/78) - Sync with nf-core tools 3.2.0
+- [PR #79](https://github.com/seqeralabs/nf-aggregate/pull/79) - nf-test auto sharding + better pipeline level test
 
 ## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-11-12
 

From 1f959eb327b214cae968bfce8f48e4577bdd9cd3 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 27 Feb 2025 11:31:43 +0100
Subject: [PATCH 3/6] fix linting

---
 .nf-core.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.nf-core.yml b/.nf-core.yml
index e19fb5b..8b5db26 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,6 +8,7 @@ lint:
     - .github/workflows/awstest.yml
     - .github/workflows/branch.yml
     - .github/workflows/linting_comment.yml
+    - .github/workflows/ci.yml
     - CODE_OF_CONDUCT.md
     - LICENSE
     - assets/email_template.html

From 4e6e100045030e60e32085acb6919ca88c98770b Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 27 Feb 2025 13:28:42 +0100
Subject: [PATCH 4/6] update CHANGELOG

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 298f4fb..0f5faed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -23,7 +23,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #74](https://github.com/seqeralabs/nf-aggregate/pull/74) - Add process for generating Benchmark reports
 - [PR #75](https://github.com/seqeralabs/nf-aggregate/pull/75) - Skip failed jobs in benchmarking report
 - [PR #78](https://github.com/seqeralabs/nf-aggregate/pull/78) - Sync with nf-core tools 3.2.0
-- [PR #79](https://github.com/seqeralabs/nf-aggregate/pull/79) - nf-test auto sharding + better pipeline level test
+- [PR #79](https://github.com/seqeralabs/nf-aggregate/pull/79) - nf-test auto sharding
 
 ## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-11-12
 

From b969276cb058aad9909948a26ced5e921e9adb41 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 27 Feb 2025 13:30:40 +0100
Subject: [PATCH 5/6] remove unused test tags

---
 modules/local/plot_run_gantt/tests/tags.yml                 | 2 --
 modules/local/seqera_runs_dump/tests/tags.yml               | 2 --
 modules/nf-core/multiqc/tests/tags.yml                      | 2 --
 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml | 2 --
 tests/tags.yml                                              | 5 -----
 5 files changed, 13 deletions(-)
 delete mode 100644 modules/local/plot_run_gantt/tests/tags.yml
 delete mode 100644 modules/local/seqera_runs_dump/tests/tags.yml
 delete mode 100644 modules/nf-core/multiqc/tests/tags.yml
 delete mode 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
 delete mode 100644 tests/tags.yml

diff --git a/modules/local/plot_run_gantt/tests/tags.yml b/modules/local/plot_run_gantt/tests/tags.yml
deleted file mode 100644
index ce481c7..0000000
--- a/modules/local/plot_run_gantt/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-plot_run_gantt:
-  - modules/local/plot_run_gantt/**
diff --git a/modules/local/seqera_runs_dump/tests/tags.yml b/modules/local/seqera_runs_dump/tests/tags.yml
deleted file mode 100644
index 2983b13..0000000
--- a/modules/local/seqera_runs_dump/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-seqera_runs_dump:
-  - modules/local/seqera_runs_dump/**
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
deleted file mode 100644
index bea6c0d..0000000
--- a/modules/nf-core/multiqc/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-multiqc:
-  - modules/nf-core/multiqc/**
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
deleted file mode 100644
index f847611..0000000
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-subworkflows/utils_nextflow_pipeline:
-  - subworkflows/nf-core/utils_nextflow_pipeline/**
diff --git a/tests/tags.yml b/tests/tags.yml
deleted file mode 100644
index c2e26f4..0000000
--- a/tests/tags.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-pipeline_nf-aggregate:
-  - "**.nf"
-  - "**.config"
-  - "**.nf.test"
-  - "**.json"

From afc0d7cdc4be9e1f33009a7e6d38c91aa27cbd02 Mon Sep 17 00:00:00 2001
From: maxulysse <max.u.garcia@gmail.com>
Date: Thu, 27 Feb 2025 13:31:56 +0100
Subject: [PATCH 6/6] update nf-test config file

---
 nf-test.config | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/nf-test.config b/nf-test.config
index 97ad11b..ac6caff 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,13 +1,16 @@
 config {
-    // location for all nf-tests
+    // location for all nf-test tests
     testsDir "."
 
     // nf-test directory including temporary files for each test
-    workDir System.getenv("TMPDIR") ?: '.nf-test'
+    workDir System.getenv("NFT_WORKDIR") ?: ".nf-test"
 
     // location of an optional nextflow.config file specific for executing tests
     configFile "tests/nextflow.config"
 
-    // run all test with the defined docker profile from the main nextflow.config
+    // run all test with defined profile(s) from the main nextflow.config
     profile "test"
+
+    // list of filenames or patterns that should be trigger a full test run
+    triggers 'nextflow.config', 'nf-test.config', 'tests/nextflow.config'
 }