Merge pull request #347 from nf-core/dev

Dev -> Master 2.5.0

Author: edmundmiller

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/CODEOWNERS

@@ -0,0 +1 @@
+* @nf-core/methylseq

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/methylseq then the best place to ask is on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/methylseq then the best place to ask is on the nf-core Slack [#methylseq](https://nfcore.slack.com/channels/methylseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 
@@ -116,4 +118,3 @@ 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/awsfulltest.yml

@@ -17,19 +17,24 @@ jobs:
         aligner: ["bismark", "bismark_hisat", "bwameth"]
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }}
           parameters: |
             {
-              "aligner": "${{ matrix.aligner }}",
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-${{ github.sha }}/${{matrix.aligner}}"
+              "aligner": "${{ matrix.aligner }}",
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -15,19 +15,23 @@ jobs:
     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
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/methylseq/work-${{ github.sha }}
           parameters: |
             {
               "aligner": "${{ matrix.aligner }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/methylseq/results-test-${{ github.sha }}/${{matrix.aligner}}"
             }
-          profiles: test,aws_tower
+          profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/ci.yml

@@ -21,58 +21,59 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  define_nxf_versions:
+    name: Choose nextflow versions to test against depending on target branch
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.nxf_versions.outputs.matrix }}
+    steps:
+      - id: nxf_versions
+        run: |
+          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+            echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
+          else
+            echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
+          fi
+
   test:
     name: Run pipeline with test data
+    needs: define_nxf_versions
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        NXF_VER:
-          - "22.10.1"
-          - "latest-everything"
-        aligner:
+        NXF_VER: ${{ fromJson(needs.define_nxf_versions.outputs.matrix) }}
+        test_tags:
           - "bismark"
           - "bismark_hisat"
           - "bwameth"
         profile:
           - "docker"
-    steps:
-      # Skip if it's a pull_request to dev and NXF_VER is '22.10.1'
-      - name: Skip condition
-        id: condition
-        run: |
-          if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
-            echo "skip=true" >> $GITHUB_OUTPUT
-          fi
 
+    steps:
       - name: Check out pipeline code
-        if: steps.condition.outputs.skip != 'true'
         uses: actions/checkout@v3
 
       - name: Hash Github Workspace
-        if: steps.condition.outputs.skip != 'true'
         id: hash_workspace
         run: |
           echo "digest=$(echo methylseq2_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
 
       - name: Cache test data
-        if: steps.condition.outputs.skip != 'true'
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
           key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
-        if: steps.cache-testdata.outputs.cache-hit != 'true' && steps.condition.outputs.skip != 'true'
         uses: actions/checkout@v3
         with:
           repository: nf-core/test-datasets
           ref: methylseq
           path: test-datasets/
 
       - name: Replace remote paths in samplesheets
-        if: steps.condition.outputs.skip != 'true'
         run: |
           for f in ./test-datasets/samplesheet/*csv; do
             sed -i 's=https://github.com/nf-core/test-datasets/raw/methylseq/=./test-datasets/=g' $f
@@ -83,25 +84,27 @@ jobs:
           done;
 
       - name: Install Nextflow
-        if: steps.condition.outputs.skip != 'true'
         uses: nf-core/setup-nextflow@v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Install nf-test
-        if: steps.condition.outputs.skip != 'true'
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER
           sudo mv nf-test /usr/local/bin/
 
       - name: Run nf-test
-        if: steps.condition.outputs.skip != 'true'
         run: |
-          nf-test test tests/pipeline/${{ matrix.aligner }}/ --profile "test,${{ matrix.profile }}" --tap=test.tap
+          nf-test test --tag ${{ matrix.test_tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml
 
-      # If the test fails, output the software_versions.yml using the 'batcat' utility
       - name: Output log on failure
         if: failure()
         run: |
           sudo apt install bat > /dev/null
           batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/output/pipeline_info/software_versions.yml
+
+      - 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

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/bluesky-post-action@v0.0.2
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #

.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack