Release pixelator 2.0

.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

@@ -36,32 +36,23 @@ jobs:
           - "24.04.2"
           - "latest-everything"
         filter: ["workflow", "function", "pipeline"]
-        profile: ["conda", "docker", "singularity"]
+        # TODO: Add conda back when pixelator is available on bioconda again
+        profile: ["docker", "singularity"]
         shard: [1, 2, 3, 4, 5]
         isMaster:
           - ${{ github.base_ref == 'master' }}
         exclude:
-          - isMaster: false
-            profile: "conda"
+          # - isMaster: false
+          #   profile: "conda"
           - isMaster: false
             profile: "singularity"
 
     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 +74,7 @@ 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 +101,8 @@ 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
@@ -21,4 +24,4 @@ template:
     - fastqc
     - multiqc
     - igenomes
-  version: 1.4.0
+  version: 2.0.0

.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

.vscode/settings.json

@@ -1,3 +1,7 @@
 {
-    "markdown.styles": ["public/vscode_markdown.css"]
+    "markdown.styles": [
+        "public/vscode_markdown.css"
+    ],
+    "nextflow.formatting.harshilAlignment": true
 }
+

CHANGELOG.md

@@ -3,6 +3,77 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[2.0.0](https://github.com/nf-core/pixelator/releases/tag/2.0.0)] - 2025-06-23
+
+This release is a major update of the nf-core/pixelator pipeline. It brings in support for the
+Proximity Network Analysis (PNA) workflow in addition to the Molecular Pixelation (MPX) workflow.
+Any run of the pipeline will now run the appropriate workflow depending on which design is specified in the input samplesheet.
+
+### Enhancements & fixes
+
+- [[PR #131](https://github.com/nf-core/pixelator/pull/131)] - Update to pixelator 0.20.1, and add PNA workflows
+- [[PR #132](https://github.com/nf-core/pixelator/pull/132)] - Template update for nf-core/tools v3.2.1
+- [[PR #133](https://github.com/nf-core/pixelator/pull/133)] - Documentation updates
+
+### Parameters
+
+| Old parameter | New parameter                                               |
+| ------------- | ----------------------------------------------------------- |
+|               | `--save_pna_demux_parquet`                                  |
+|               | `--save_pna_demux_passed_reads`                             |
+|               | `--save_pna_demux_failed_reads`                             |
+|               | `--save_pna_collapsed_reads`                                |
+|               | `--save_pna_graph_pixelfile`                                |
+|               | `--save_pna_analysis_pixelfile`                             |
+|               | `--save_json`                                               |
+|               | `--pna_amplicon_mismatches`                                 |
+|               | `--pna_amplicon_remove_polyg`                               |
+|               | `--pna_amplicon_quality_cutoff`                             |
+|               | `--pna_demux_mismatches`                                    |
+|               | `--pna_demux_output_chunk_reads`                            |
+|               | `--pna_demux_output_max_chunks`                             |
+|               | `--pna_demux_strategy`                                      |
+|               | `--pna_collapse_mismatches`                                 |
+|               | `--pna_collapse_algorithm`                                  |
+|               | `--pna_graph_multiplet_recovery`                            |
+|               | `--pna_graph_leiden_iterations`                             |
+|               | `--pna_graph_initial_stage_leiden_resolution`               |
+|               | `--pna_graph_refinement_stage_leiden_resolution`            |
+|               | `--pna_graph_min_count`                                     |
+|               | `--pna_graph_min_component_size_in_refinement`              |
+|               | `--pna_graph_max_refinement_recursion_depth`                |
+|               | `--pna_graph_initial_stage_max_edges_to_remove`             |
+|               | `--pna_graph_refinement_stage_max_edges_to_remove`          |
+|               | `--pna_graph_initial_stage_max_edges_to_remove_relative`    |
+|               | `--pna_graph_refinement_stage_max_edges_to_remove_relative` |
+|               | `--pna_graph_graph_min_component_size_to_prune`             |
+|               | `--pna_graph_component_size_min_threshold`                  |
+|               | `--pna_analysis_compute_proximity`                          |
+|               | `--pna_analysis_proximity_nbr_of_permutations`              |
+|               | `--pna_analysis_compute_k_cores`                            |
+|               | `--pna_analysis_compute_svd_var_explained`                  |
+|               | `--pna_analysis_svd_nbr_of_pivots`                          |
+|               | `--pna_layout_no_node_marker_counts`                        |
+|               | `--pna_layout_layout_algorithm`                             |
+|               | `--pna_layout_pmds_pivots`                                  |
+|               | `--pna_layout_wpmds_k`                                      |
+
+> [!NOTE]
+> Parameter has been **updated** if both old and new parameter information is present.
+> Parameter has been **added** if just the new parameter information is present.
+> Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `pixelator` | 0.19.0      | 0.20.1      |
+
+> [!NOTE]
+> Dependency has been **updated** if both old and new parameter information is present.
+> Dependency has been **added** if just the new parameter information is present.
+> Dependency has been **removed** if new parameter information isn't present.
+
 ## [[1.4.0](https://github.com/nf-core/pixelator/releases/tag/1.4.0)] - 2024-01-22
 
 ### Enhancements & fixes