Add nextflow-lint pre-commit hook

.github/workflows/lint.yml

@@ -30,12 +30,14 @@ env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
   NXF_VER: "25.10.2"
+  NXF_SYNTAX_PARSER: "v2"
 
 jobs:
   pre-commit:
     runs-on: ${{ github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted' }}
     steps:
       - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: nf-core/setup-nextflow@v2
       - name: Run prek
         uses: j178/prek-action@0bb87d7f00b0c99306c8bcb8b8beba1eb581c037 # v1
 

.pre-commit-config.yaml

@@ -60,3 +60,11 @@ repos:
     hooks:
       - id: hadolint-docker
         args: ["--failure-threshold", "error"]
+
+  - repo: https://github.com/seqeralabs/nf-lint-pre-commit
+    rev: v0.2.0
+    hooks:
+      - id: nextflow-lint
+        files: '\.nf$|nextflow\.config$'
+        # TODO add formating at a later stage
+        # args: ["-format", "-sort-declarations", "-spaces", "4", "-harshil-alignment", "-output", "concise"]

modules/nf-core/coverm/genome/tests/nextflow.config

@@ -1,8 +1,6 @@
 process {
     withName: COVERM_GENOME {
-    ext {
-        reference_mode = 'dir'   // force directory branch
-        args = '--genome-fasta-extension fasta'
-        }
+        ext.reference_mode = 'dir' // force directory branch
+        ext.args = '--genome-fasta-extension fasta'
     }
 }