moved cellpose properties under segmentation

tried to cleanup some lint errors

.github/workflows/ci.yml

@@ -26,15 +26,21 @@ jobs:
         NXF_VER:
           - "24.10.4"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
-
+  
       - name: Run pipeline with test data
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
 
@@ -31,35 +31,49 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
+      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
         with:
           python-version: "3.12"
           architecture: "x64"
 
+      - name: read .nf-core.yml
+        uses: pietrobolcato/[email protected]
+        id: read_yml
+        with:
+          config: ${{ github.workspace }}/.nf-core.yml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install nf-core
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
-      - name: Run nf-core lint
+      - name: Run nf-core pipelines lint
         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' }}
+        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 --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
       - name: Save PR number
         if: ${{ always() }}
         run: echo ${{ github.event.pull_request.number }} > PR_number.txt
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4
         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@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.gitignore

@@ -6,6 +6,5 @@ results/
 testing/
 testing*
 *.pyc
-mylocal
-lint_log.txt
-
+null/
+mylocal

.nf-core.yml

@@ -1,28 +1,20 @@
+repository_type: pipeline
+
+nf_core_version: 3.2.0
+
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md
-    - assets/nf-core-janeliascicomp-easifish_logo_light.png
-    - docs/images/nf-core-janeliascicomp-easifish_logo_light.png
-    - docs/images/nf-core-janeliascicomp-easifish_logo_dark.png
     - .github/ISSUE_TEMPLATE/config.yml
-    - .github/workflows/awstest.yml
-    - .github/workflows/awsfulltest.yml
-    - conf/igenomes.config
   files_unchanged:
     - LICENSE
     - CODE_OF_CONDUCT.md
-    - assets/nf-core-janeliascicomp-easifish_logo_light.png
-    - docs/images/nf-core-janeliascicomp-easifish_logo_light.png
-    - docs/images/nf-core-janeliascicomp-easifish_logo_dark.png
     - .github/ISSUE_TEMPLATE/bug_report.yml
   nextflow_config:
     - manifest.name
     - manifest.homePage
-  multiqc_config: False
   readme:
     - nextflow_badge
-nf_core_version: 2.14.1
-repository_type: pipeline
 template:
   prefix: JaneliaSciComp
   skip:

.prettierignore

@@ -10,3 +10,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json

nextflow.config

@@ -59,12 +59,8 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
+// Load nf-core custom profiles from different Institutions.
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Override institutional configs which set scratch dir, since that results in large data being copied instead of symlinked
 process {

nextflow_schema.json

@@ -704,6 +704,30 @@
                     "type": "boolean",
                     "description": "If true skip segmentation"
                 },
+                "sample_anisotropy": {
+                    "type": "number",
+                    "default": 1.0
+                },
+                "sample_expansion_factor": {
+                    "type": "number",
+                    "default": 1.0
+                },
+                "sample_voxel_spacing": {
+                    "type": "string"
+                },
+                "sample_z_axis": {
+                    "type": "integer",
+                    "default": 0
+                },
+                "cellpose_verbose": {
+                    "type": "boolean"
+                },
+                "cellpose_preprocessing_steps": {
+                    "type": "string"
+                },
+                "cellpose_preprocessing_params_file": {
+                    "type": "string"
+                },
                 "distributed_cellpose": {
                     "type": "boolean",
                     "description": "Use a distributed dask cluster to run segmentation",
@@ -850,6 +874,13 @@
                     "default": 0,
                     "description": "Default dashboards port of the Dask segmentation cluster",
                     "hidden": true
+                },
+                "cellpose_worker_runtime_opts": {
+                    "type": "string"
+                },
+                "cellpose_worker_lsf_opts": {
+                    "type": "string",
+                    "default": "-q gpu_l4 -gpu \"num=1"
                 }
             }
         },
@@ -1002,38 +1033,5 @@
         {
             "$ref": "#/definitions/generic_options"
         }
-    ],
-    "properties": {
-        "sample_anisotropy": {
-            "type": "integer",
-            "default": 1
-        },
-        "sample_expansion_factor": {
-            "type": "integer",
-            "default": 1
-        },
-        "sample_voxel_spacing": {
-            "type": "string"
-        },
-        "sample_z_axis": {
-            "type": "integer",
-            "default": 0
-        },
-        "cellpose_verbose": {
-            "type": "boolean"
-        },
-        "cellpose_preprocessing_steps": {
-            "type": "string"
-        },
-        "cellpose_preprocessing_params_file": {
-            "type": "string"
-        },
-        "cellpose_worker_runtime_opts": {
-            "type": "string"
-        },
-        "cellpose_worker_lsf_opts": {
-            "type": "string",
-            "default": "-q gpu_l4 -gpu \"num=1"
-        }
-    }
+    ]
 }