Important! Template update for nf-core/tools v3.2.1

.github/workflows/awsfulltest.yml

@@ -4,57 +4,36 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/pixelator' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
+    if: github.repository == 'nf-core/pixelator' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         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/pixelator/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/pixelator/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pixelator/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pixelator/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 

.github/workflows/ci.yml

@@ -48,20 +48,10 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
         with:
           fetch-depth: 0
 
-      - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-
-      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
-        with:
-          distribution: "temurin"
-          java-version: "17"
-
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
@@ -83,7 +73,7 @@ jobs:
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
       - name: Cache pdiff
-        uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4
+        uses: actions/cache@v4
         id: cache-pip-pdiff
         with:
           path: ~/.cache/pip
@@ -110,8 +100,8 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
-      - name: Start summary
-        id: print-test
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
           echo "## nf-test tests summary :rocket:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        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:

.nf-core.yml

@@ -1,13 +1,16 @@
 lint:
   actions_ci: false
-  multiqc_config: false
-  files_unchanged:
-    - assets/nf-core-pixelator_logo_light.png
   files_exist:
     - assets/multiqc_config.yml
     - conf/igenomes.config
     - conf/igenomes_ignored.config
-nf_core_version: 3.1.1
+  files_unchanged:
+    - assets/nf-core-pixelator_logo_light.png
+    # Ignore this for now since we haven't switched the name of the
+    # main branch to main from master yet
+    - .github/PULL_REQUEST_TEMPLATE.md
+  multiqc_config: false
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: Pixelgen Technologies AB

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
           - prettier@3.2.5
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec

README.md

@@ -3,8 +3,12 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-pixelator_logo_dark.png">
     <img alt="nf-core/pixelator" src="docs/images/nf-core-pixelator_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112)
+</h1>
+
+[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)
@@ -40,7 +44,7 @@ It takes a samplesheet as input and will process your data using `pixelator` to
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 First, prepare a samplesheet with your input data that looks as follows:
 

conf/test.config

@@ -14,16 +14,16 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '15.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 }
 
 aws.client.downloadParallel = true
 
 
 params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name               = 'Test profile'
+    config_profile_description        = 'Minimal test dataset to check pipeline function'
 
     // Input data
     input                             = params.pipelines_testdata_base_path + 'samplesheet/samplesheet.csv'

main.nf

@@ -41,7 +41,6 @@ workflow NFCORE_PIXELATOR {
     PIXELATOR (
         samplesheet
     )
-    // TODO: Emit MultiQC report once implemented
 }
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -82,7 +81,6 @@ workflow {
         params.outdir,
         params.monochrome_logs,
         params.hook_url,
-        []
     )
 }
 

nextflow.config

@@ -274,7 +274,8 @@ process.shell = [
     "-C",         // No clobber - prevent output redirection from overwriting files.
     "-e",         // Exit if a tool returns a non-zero status/exit code
     "-u",         // Treat unset variables and parameters as an error
-    "-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
 ]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
@@ -339,7 +340,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

ro-crate-metadata.json

@@ -127,14 +127,10 @@
         },
         {
             "@id": "main.nf",
-            "@type": [
-                "File",
-                "SoftwareSourceCode",
-                "ComputationalWorkflow"
-            ],
+            "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "creator": [
                 {
-                    "@id": "#florian.detemmerman@pixelgen.com"
+                    "@id": "https://orcid.org/0009-0006-0086-2470"
                 }
             ],
             "dateCreated": "",
@@ -150,25 +146,16 @@
                 "single-cell",
                 "single-cell-omics"
             ],
-            "license": [
-                "MIT"
-            ],
-            "name": [
-                "nf-core/pixelator"
-            ],
+            "license": ["MIT"],
+            "name": ["nf-core/pixelator"],
             "programmingLanguage": {
                 "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow"
             },
             "sdPublisher": {
                 "@id": "https://nf-co.re/"
             },
-            "url": [
-                "https://github.com/nf-core/pixelator",
-                "https://nf-co.re/pixelator/1.4.0/"
-            ],
-            "version": [
-                "1.4.0"
-            ]
+            "url": ["https://github.com/nf-core/pixelator", "https://nf-co.re/pixelator/dev/"],
+            "version": ["1.5.0dev"]
         },
         {
             "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow",
@@ -335,10 +322,10 @@
             "url": "https://nf-co.re/"
         },
         {
-            "@id": "#florian.detemmerman@pixelgen.com",
+            "@id": "https://orcid.org/0009-0006-0086-2470",
             "@type": "Person",
             "email": "florian.detemmerman@pixelgen.com",
             "name": "Florian De Temmerman"
         }
     ]
-}
+}