Merge pull request #1199 from nf-core/dev

Candidate release 3.3.0

.github/CONTRIBUTING.md

@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

.github/workflows/awstest.yml

@@ -3,27 +3,59 @@ name: nf-core AWS test
 # It runs the -profile 'test' on AWS batch
 
 on:
+  release:
+    types: [created]
   workflow_dispatch:
+    inputs:
+      profiletest:
+        description: "Trigger profile tests (smaller) on AWS"
+        type: boolean
+        default: true
+      somatic:
+        description: "Trigger somatic full test on AWS"
+        type: boolean
+        default: false
+      germline:
+        description: "Trigger germline full test on AWS"
+        type: boolean
+        default: false
+
 jobs:
-  run-tower:
+  trigger-profile-test:
     name: Run AWS tests
-    if: github.repository == 'nf-core/sarek'
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - profile: test
+            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.profiletest ) }}
+          - profile: test_full
+            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.somatic ) }}
+          - profile: test_full_germline
+            enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || inputs.germline ) }}
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
+        if: ${{ matrix.enabled }}
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/sarek/work-${{ github.sha }}/${{ matrix.profile }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}/${{ matrix.profile }}"
             }
-          profiles: test
+          profiles: ${{ matrix.profile }}
+
       - uses: actions/upload-artifact@v3
+        if: ${{ matrix.enabled }}
         with:
-          name: Tower debug log file
-          path: tower_action_*.log
+          name: tower-${{ matrix.profile }}-log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/ci.yml

@@ -1,37 +1,55 @@
-name: nf-core CI
+name: test
 # 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]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
 
 # Cancel if a newer run is started
 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:
+      # Expose matched filters as job 'tags' output variable
+      tags: ${{ steps.filter.outputs.changes }}
+    steps:
+      - uses: actions/checkout@v3
+      - uses: dorny/paths-filter@v2
+        id: filter
+        with:
+          filters: "tests/config/tags.yml"
+
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}"
+    name: ${{ matrix.tags }} ${{ matrix.profile }} NF ${{ matrix.NXF_VER }}
     runs-on: ubuntu-latest
+    needs: changes
+    if: needs.changes.outputs.tags != '[]'
     strategy:
-      # HACK Remove after DSL2 rewrite is done
       fail-fast: false
       matrix:
+        tags: ["${{ fromJson(needs.changes.outputs.tags) }}"]
+        profile: ["docker"]
+        # profile: ["docker", "singularity", "conda"]
+        TEST_DATA_BASE:
+          - "test-datasets/data"
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        test:
-          - "default"
-        profile: ["docker"]
-        # profile: ["docker", "singularity", "conda"]
     env:
       NXF_ANSI_LOG: false
       TEST_DATA_BASE: "${{ github.workspace }}/test-datasets"
+      SENTIEON_LICENSE_BASE64: ${{ secrets.SENTIEON_LICENSE_BASE64 }}
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -41,6 +59,36 @@ jobs:
         run: |
           echo "digest=$(echo sarek3_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
 
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.x"
+          cache: "pip"
+          cache-dependency-path: |
+            **/requirements.txt
+
+      - name: Install Python dependencies
+        run: pip install --upgrade -r tests/requirements.txt
+
+      - name: Install Nextflow ${{ matrix.NXF_VER }}
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
+
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-singularity@v5
+        with:
+          singularity-version: 3.7.1
+
+      - name: Set up miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          channels: conda-forge,bioconda,defaults
+          python-version: ${{ matrix.python-version }}
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
@@ -65,55 +113,26 @@ jobs:
             echo "========================================"
           done;
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: "3.x"
-
-      - uses: actions/cache@v3
-        with:
-          path: ~/.cache/pip
-          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
-          restore-keys: |
-            ${{ runner.os }}-pip-
-
-      - name: Install Python dependencies
-        run: python -m pip install --upgrade pip pytest-workflow
-
-      - uses: actions/cache@v3
-        with:
-          path: /usr/local/bin/nextflow
-          key: ${{ runner.os }}
-          restore-keys: |
-            ${{ runner.os }}-nextflow-
-
-      - name: Install Nextflow ${{ matrix.NXF_VER }}
-        uses: nf-core/setup-nextflow@v1.2.0
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Set up Singularity
-        if: matrix.profile == 'singularity'
-        uses: eWaterCycle/setup-singularity@v5
-        with:
-          singularity-version: 3.7.1
-
-      - name: Set up miniconda
-        if: matrix.profile == 'conda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          channels: conda-forge,bioconda,defaults
-          python-version: ${{ matrix.python-version }}
+      # Set up secrets
+      - name: Set up nextflow secrets
+        if: env.SENTIEON_LICENSE_BASE64 != null
+        run: |
+          nextflow secrets set SENTIEON_LICENSE_BASE64 ${{ secrets.SENTIEON_LICENSE_BASE64 }}
+          nextflow secrets set SENTIEON_AUTH_MECH_BASE64 ${{ secrets.SENTIEON_AUTH_MECH_BASE64 }}
+          SENTIEON_ENCRYPTION_KEY=$(echo -n "${{ secrets.ENCRYPTION_KEY_BASE64 }}" | base64 -d)
+          SENTIEON_LICENSE_MESSAGE=$(echo -n "${{ secrets.LICENSE_MESSAGE_BASE64 }}" | base64 -d)
+          SENTIEON_AUTH_DATA=$(python bin/license_message.py encrypt --key "$SENTIEON_ENCRYPTION_KEY" --message "$SENTIEON_LICENSE_MESSAGE")
+          SENTIEON_AUTH_DATA_BASE64=$(echo -n "$SENTIEON_AUTH_DATA" | base64 -w 0)
+          nextflow secrets set SENTIEON_AUTH_DATA_BASE64 $SENTIEON_AUTH_DATA_BASE64
 
       - name: Conda clean
         if: matrix.profile == 'conda'
         run: conda clean -a
 
-      - name: Run pipeline with tests settings
-        uses: Wandalen/wretry.action@v1.0.11
+      - name: Run pytest-workflow
+        uses: Wandalen/wretry.action@v1
         with:
-          command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes
+          command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes
           attempt_limit: 3
 
       - name: Output log on failure
@@ -134,3 +153,22 @@ jobs:
             /home/runner/pytest_workflow_*/*/work
             !/home/runner/pytest_workflow_*/*/work/conda
             !/home/runner/pytest_workflow_*/*/work/singularity
+
+  confirm-pass:
+    runs-on: ubuntu-latest
+    needs:
+      - test
+    if: always()
+    steps:
+      - name: All tests ok
+        if: ${{ success() || !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) }}"