Release 6.0.0

.github/actions/get-shards/action.yml

@@ -21,7 +21,7 @@ runs:
   using: "composite"
   steps:
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
+      uses: nf-core/setup-nf-test@v2
       with:
         version: ${{ env.NFT_VER }}
     - name: Get number of shards

.github/actions/nf-test/action.yml

@@ -20,24 +20,24 @@ runs:
   using: "composite"
   steps:
     - name: Setup Nextflow
-      uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+      uses: nf-core/setup-nextflow@v3
       with:
         version: "${{ env.NXF_VERSION }}"
 
     - name: Set up Python
-      uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+      uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7
       with:
-        python-version: "3.14"
+        python-version: "3.15"
 
     - name: Install nf-test
-      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
+      uses: nf-core/setup-nf-test@v2
       with:
         version: "${{ env.NFT_VER }}"
         install-pdiff: true
 
     - name: Setup apptainer
       if: contains(inputs.profile, 'singularity')
-      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2.0.0
+      uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
 
     - name: Set up Singularity
       if: contains(inputs.profile, 'singularity')
@@ -48,7 +48,7 @@ runs:
 
     - name: Conda setup
       if: contains(inputs.profile, 'conda')
-      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
+      uses: conda-incubator/setup-miniconda@be893c923ea9cf1cf7cd510fbdde27c7e18cbdcb # v4.1.0
       with:
         auto-update-conda: true
         conda-solver: libmamba

.github/workflows/awsfulltest.yml

@@ -23,7 +23,7 @@ jobs:
           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@9856f1ae20c8b02884733f79b7cd0e3ea5d2bdab # v2.4
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -57,7 +57,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Seqera Platform CLI tool action
       - name: Launch workflow via Seqera Platform
-        uses: seqeralabs/action-tower-launch@9856f1ae20c8b02884733f79b7cd0e3ea5d2bdab # v2.4
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+      - uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/branch.yml

@@ -56,7 +56,7 @@ jobs:
 
       - name: Upload PR comment artifact
         if: failure()
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: pr-comment
           path: pr-comment/

.github/workflows/download_pipeline.yml

@@ -42,18 +42,18 @@ jobs:
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+        uses: nf-core/setup-nextflow@v3
 
       - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        uses: jlumbroso/free-disk-space@ceedf095f4ec1a097402bc6bd80831f2e1a6fde6 # v2.0.0
 
-      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+      - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7
         with:
-          python-version: "3.14"
+          python-version: "3.15"
           architecture: "x64"
 
       - name: Setup Apptainer
-        uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
+        uses: eWaterCycle/setup-apptainer@3f706d898c9db585b1d741b4692e66755f3a1b40 # v2
         with:
           apptainer-version: 1.3.6
 
@@ -135,7 +135,7 @@ jobs:
           fi
 
       - name: Upload Nextflow logfile for debugging purposes
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: nextflow_logfile.txt
           path: .nextflow.log*

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+        uses: nf-core/setup-nextflow@v3
 
       - name: Run prek
-        uses: j178/prek-action@5337cb91e0fa35a7ff31b9ca345126d8bbbcdf16 # v2
+        uses: j178/prek-action@44924fe9ef4a6f88253c4b6b1bf11c689d3ce53d # v3.1.0
 
   nf-core:
     runs-on: ubuntu-latest
@@ -26,15 +26,15 @@ jobs:
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@893c28b667aedeba26e37f296d260ccc5bc4d914 # v3
+        uses: nf-core/setup-nextflow@v3
 
-      - uses: actions/setup-python@5fda3b95a4ea91299a34e894583c3862153e4b97 # v7
+      - uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7
         with:
-          python-version: "3.14"
+          python-version: "3.15"
           architecture: "x64"
 
       - name: Setup uv
-        uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
+        uses: astral-sh/setup-uv@07a047e608db84b3d8c06cd9a7c7dcc9c355c18e # v10.3.2
 
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
@@ -67,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: linting-logs
           path: |
@@ -88,7 +88,7 @@ jobs:
 
       - name: Upload PR comment artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: pr-comment
           path: pr-comment/

.github/workflows/nf-test.yml

@@ -129,7 +129,7 @@ jobs:
 
       - name: Upload PR comment fragment
         if: ${{ always() && steps.run_nf_test.outcome == 'failure' && matrix.NXF_VER == 'latest-everything' }}
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
         with:
           name: pr-comment-fragment-${{ strategy.job-index }}
           path: pr-comment-fragment/
@@ -163,7 +163,7 @@ jobs:
 
       - name: Download PR comment fragments
         if: ${{ always() }}
-        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        uses: actions/download-artifact@9000827ccba6bdab643e8b6fd33ac0654aef8333 # v8.0.2
         continue-on-error: true
         with:
           pattern: pr-comment-fragment-*
@@ -197,7 +197,7 @@ jobs:
 
       - name: Upload PR comment artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7
         with:
           name: pr-comment
           path: pr-comment/

.github/workflows/pr-comment.yml

@@ -31,7 +31,7 @@ jobs:
     if: github.event.workflow_run.event == 'pull_request'
     steps:
       - name: Download PR comment artifact
-        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
+        uses: dawidd6/action-download-artifact@eab87c9830c39eff17e5a6eadb20bfb4bc880477 # v27
         with:
           run_id: ${{ github.event.workflow_run.id }}
           name: pr-comment

.github/workflows/template-version-comment.yml

@@ -54,7 +54,7 @@ jobs:
           fi
 
       - name: Upload PR comment artifact
-        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
         with:
           name: pr-comment
           path: pr-comment/

.gitignore

@@ -11,3 +11,5 @@ null/
 .vscode
 .nf-test*
 .lineage/
+.nf-test/
+.nf-test.log

.nf-core.yml

@@ -13,7 +13,7 @@ lint:
     - .github/workflows/branch.yml
     - .github/workflows/linting.yml
   multiqc_config: false
-nf_core_version: 4.1.0
+nf_core_version: 4.2.1
 repository_type: pipeline
 template:
   author: Pixelgen Technologies AB
@@ -27,4 +27,4 @@ template:
     - fastqc
     - multiqc
     - igenomes
-  version: 5.0.3
+  version: 6.0.0

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.9.6
+          - prettier@3.9.10
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:

.vscode/extensions.json

@@ -0,0 +1,12 @@
+{
+    // See https://github.com/nf-core/vscode-extensionpack
+    "recommendations": [
+        "codezombiech.gitignore",
+        "esbenp.prettier-vscode",
+        "jebbs.markdown-extended",
+        "mechatroner.rainbow-csv",
+        "nextflow.nextflow",
+        "onnovalkering.vscode-singularity",
+        "redhat.vscode-yaml"
+    ]
+}

.vscode/settings.json

@@ -1,6 +1,4 @@
 {
-    "markdown.styles": [
-        "public/vscode_markdown.css"
-    ],
-    "nextflow.formatting.harshilAlignment": true
+    // Render nf-core website admonitions nicely in markdown previews
+    "markdown.styles": ["https://nf-co.re/vscode_markdown.css"]
 }

CHANGELOG.md

@@ -3,6 +3,40 @@
 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).
 
+## [[6.0.0](https://github.com/nf-core/pixelator/releases/tag/6.0.0)] - 2026-11-02
+
+### Major
+
+#### Enhancements & fixes
+
+- Update pixelator to 0.31.0. By @Aratz [#270](https://github.com/nf-core/pixelator/pull/270)
+
+### Patches
+
+#### Enhancements & fixes
+
+- Setup AWS megatests. By @Aratz [#267](https://github.com/nf-core/pixelator/pull/267)
+- Update nf-core template to 4.2.1 by @Aratz [#269](https://github.com/nf-core/pixelator/pull/269)
+- Update pixelatorES to 0.15.1. By @Aratz [#270](https://github.com/nf-core/pixelator/pull/270)
+
+### Parameters
+
+| Old parameter                                  | New parameter |
+| ---------------------------------------------- | ------------- |
+| `--pna_analysis_proximity_nbr_of_permutations` |               |
+
+> [!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`   | 0.30.0      | 0.31.0      |
+| `pixelatorES` | 0.11.2      | 0.15.1      |
+
 ## [[5.0.3](https://github.com/nf-core/pixelator/releases/tag/5.0.3)] - 2026-10-07
 
 ### Patches

README.md

@@ -13,7 +13,7 @@
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.1.0-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.1.0)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-4.2.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.2.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

conf/base.config

@@ -61,7 +61,6 @@ process {
         maxRetries    = 2
     }
     withLabel: process_gpu {
-        ext.use_gpu = { workflow.profile.contains('gpu') }
         accelerator = { workflow.profile.contains('gpu') ? 1 : null }
     }
 }

conf/modules.pna.config

@@ -218,7 +218,6 @@ process {
         ext.args   = {
             [
                 params.pna_analysis_compute_proximity ? "--compute-proximity" : '',
-                params.pna_analysis_proximity_nbr_of_permutations ? "--proximity-nbr-of-permutations ${params.pna_analysis_proximity_nbr_of_permutations}" : '',
                 params.pna_analysis_compute_k_cores ? "--compute-k-cores" : '',
                 params.pna_analysis_compute_svd_var_explained ? "--compute-svd-var-explained" : '',
                 params.pna_analysis_svd_nbr_of_pivots ? "--svd-nbr-of-pivots ${params.pna_analysis_svd_nbr_of_pivots}" : '',

conf/test_full.config

@@ -1,6 +1,6 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
+    Nextflow config file for running full-size tests
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test
     for the pna pipline
@@ -11,4 +11,12 @@
 ----------------------------------------------------------------------------------------
 */
 
-includeConfig 'test_proxiome_v2.config'
+params {
+    config_profile_name                    = 'Full test profile'
+    config_profile_description             = 'Full test profile to check pipeline function'
+
+    // Input data
+    input                                  = "https://raw.githubusercontent.com/nf-core/test-datasets/f6fd3ce6cd14c0b94a4f6e26a02d9956b45824a7/new-test-data/samplesheet/pna/samplesheet_full_tests.csv"
+
+    technology                             = "proxiome-v2"
+}