[WIP] fix some actions

.github/workflows/ci.yml

@@ -53,11 +53,11 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - uses: AlexVCaron/setup-nf-test@2c5a31b90b34d97abf155b57ee0f79c7f5aa118a
-        # Used to make the action executable on our runners. Related to how the home
-        # and work directories are set up from ephemeral disks. See nf-core/setup-nf-test/issues/6
+      - name: Setup nf-test
+        uses: nf-core/[email protected]
         with:
-          version: ${{ matrix.nf_test_version }}
+          version: 0.9.2
+          install-pdiff: true
 
       - name: Set up Apptainer
         if: matrix.profile == 'singularity'

.nf-core.yml

@@ -9,6 +9,8 @@ lint:
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - conf/igenomes.config
+    - assets/FS_BN_GL_SF_utils/**
+    - assets/templates/**
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-pediatric_logo_light.png

.pre-commit-config.yaml

@@ -1,3 +1,4 @@
+exclude: 'assets/**'
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"

nextflow_schema.json

@@ -87,7 +87,6 @@
                     "fa_icon": "fas fa-folder",
                     "help_text": "Path to the utils folder. This folder contains the atlases used in the pipeline. You can download the utils folder from the nf-pediatric GitHub repository.",
                     "format": "directory-path",
-                    "default": "${projectDir}/assets/FS_BN_GL_SF_utils/",
                     "exists": true,
                     "hidden": true
                 }
@@ -167,14 +166,12 @@
                     "type": "string",
                     "description": "Path to the template to use in antsBet",
                     "fa_icon": "fas fa-brain",
-                    "default": "${projectDir}/assets/templates/t1_template.nii.gz",
                     "hidden": true
                 },
                 "t1_bet_template_probability_map": {
                     "type": "string",
                     "description": "Path to the template probability map to use in antsBet",
                     "fa_icon": "fas fa-brain",
-                    "default": "${projectDir}/assets/templates/t1_brain_probability_map.nii.gz",
                     "hidden": true
                 }
             }