Updated pipeline to run on the latest versions of Nextflow

.github/workflows/branch.yml

@@ -21,7 +21,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
+        uses: mshick/add-pr-comment@8e4927817251f1ff60c001f04568532b38e0b4a0 # v3
         with:
           message: |
             ## This PR is against the `${{github.event.pull_request.base.ref}}` branch :x:

.github/workflows/linting.yml

@@ -11,54 +11,50 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
-        with:
-          python-version: "3.13"
-
-      - name: Install pre-commit
-        run: pip install pre-commit
+      - name: Install Nextflow
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - name: Run pre-commit
-        run: pre-commit run --all-files
+      - name: Run prek
+        uses: j178/prek-action@6ad80277337ad479fe43bd70701c3f7f8aa74db3 # v2
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v2
+        uses: nf-core/setup-nextflow@b4ec1bc7c16a94435159de94a05253542fddf6ef # v3
 
-      - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
         with:
-          python-version: "3.13"
+          python-version: "3.14"
           architecture: "x64"
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@08807647e7069bb48b6ef5acd8ec9567f424441b # v8.1.0
+
       - name: read .nf-core.yml
         uses: pietrobolcato/action-read-yaml@9f13718d61111b69f30ab4ac683e67a56d254e1d # 1.1.0
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+        run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
-        if: ${{ github.base_ref != 'master' }}
+        if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
         run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
-        if: ${{ github.base_ref == 'master' }}
+        if: ${{ github.base_ref == 'master' || github.base_ref == 'main' }}
         env:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
@@ -71,7 +67,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
+        uses: dawidd6/action-download-artifact@b6e2e70617bc3265edd6dab6c906732b2f1ae151 # v21
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@52423e01640425a022ef5fd42c6fb5f633a02728 # v2
+        uses: marocchino/sticky-pull-request-comment@70d2764d1a7d5d9560b100cbea0077fc8f633987 # v3
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/nf-test.yml

@@ -76,7 +76,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.10.5"
+          - "25.10.0"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

.gitignore

@@ -7,4 +7,6 @@ testing/
 testing*
 *.pyc
 null/
+.lineage/
+.claude
 mylocal

.nf-core.yml

@@ -1,6 +1,6 @@
 repository_type: pipeline
 
-nf_core_version: 3.3.2
+nf_core_version: 4.0.2
 
 lint:
   files_unchanged:
@@ -20,8 +20,16 @@ lint:
     - validation.help.afterText
     - validation.summary.beforeText
     - validation.summary.afterText
-  multiqc_config:
-    - report_comment
+    - config_defaults:
+        # value contains single quotes that Nextflow escapes and the linter cannot round-trip
+        - params.zarr_compression_opts
+        # resolves to a machine-specific absolute path via ${projectDir}
+        - params.dask_config
+  # this pipeline does not produce a MultiQC report
+  multiqc_config: false
+  # only subworkflows (no modules) are installed from nf-core/modules, which trips
+  # the linter's requirement that every repo entry have a "modules" key
+  modules_json: false
   files_exist:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-nf-cellpose_logo_light.png
@@ -33,7 +41,7 @@ lint:
 
 template:
   org: JaneliaSciComp
-  name: nf-cellpose
+  name: nf_cellpose
   description: Cellpose segmentation pipeline
   author: Cristian Goina
   version: 1.0.0dev

.prettierignore

@@ -1,6 +1,4 @@
 email_template.html
-adaptivecard.json
-slackreport.json
 .nextflow*
 work/
 data/
@@ -10,4 +8,7 @@ testing/
 testing*
 *.pyc
 bin/
+.nf-test/
 ro-crate-metadata.json
+modules/nf-core/
+subworkflows/nf-core/

CHANGELOG.md

@@ -3,14 +3,34 @@
 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).
 
-## v1.0.0dev - [date]
+## v1.1.0 - 2026-07-01
+
+### `Added`
+
+- Nextflow V2 parser compliance
+- Zarr v3 support
+- Conda configuration - allows one to run the pipeline using a conda profile
+
+### `Changed`
+- The pipeline requires Nextflow 25.10.0 because of updated nf-schema plugin
+
+### `Dependencies`
+- Nextflow 25.10.0
+
+## v1.0.0 - 2025-09-08
 
 Initial release of JaneliaSciComp/nf-cellpose, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
-### `Fixed`
+- Dask support
+- CellposeSAM support
 
 ### `Dependencies`
-
-### `Deprecated`
+- Nextflow 25.04.04
+- Modules:
+    - JaneliaSciComp/nextflow-modules:segtools/distributed/cellpose
+    - JaneliaSciComp/nextflow-modules:segtools/distributed/cellpose
+    - JaneliaSciComp/nextflow-modules:omezarrtools/multiscale
+- Sumworkflows:
+    - JaneliaSciComp/nextflow-modules:dask_[start,stop]

README.md

@@ -4,7 +4,7 @@
 [![GitHub Actions Linting Status](https://github.com/JaneliaSciComp/nf-cellpose/actions/workflows/linting.yml/badge.svg)](https://github.com/JaneliaSciComp/nf-cellpose/actions/workflows/linting.yml)[![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/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-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-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![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/)
@@ -33,6 +33,14 @@ nextflow run JaneliaSciComp/nf-cellpose \
    --outdir <OUTDIR>
 ```
 
+To run with conda:
+```bash
+nextflow run JaneliaSciComp/nf-cellpose \
+   -profile conda -with-conda conf/conda-env.yml \
+   --input input.ome.zarr \
+   --outdir <OUTDIR>
+```
+
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option; an example of such file is available [here](examples/segtest_sample.json). Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 

conf/conda-env.yml

@@ -1,8 +1,9 @@
 channels:
   - conda-forge
+  - bioconda
 dependencies:
   - python=3.12
   - pip
   - psutil>=7.1.3
   - pip:
-    - git+https://github.com/JaneliaSciComp/cellpose-tools@695281d
+    - git+https://github.com/JaneliaSciComp/cellpose-tools@969f729

conf/conda.config

@@ -0,0 +1,9 @@
+process {
+    withName: "(.*)SEGMENTATION:(.*)" {
+        container = null
+    }
+
+    withName: "(.*):MULTISCALE:(.*)" {
+        container = null
+    }
+}