Swapping your Snakemake --lint for Snakefmt

.github/workflows/test-snake.yml

@@ -21,16 +21,15 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Lint Code Base
+      # Run Super-Linter only on Snakefile and .smk files
+      - name: Lint Snakefiles Only
         uses: github/super-linter/slim@v5
         env:
-          VALIDATE_ALL_CODEBASE: false
-          DEFAULT_BRANCH: branch_name
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          DISABLE_ERRORS: true
-          PYTHON_FLAKE8_CONFIG_FILE: .flake8
-          VALIDATE_PYTHON_FLAKE8: true
           VALIDATE_SNAKEMAKE_SNAKEFMT: true
+          FILTER_REGEX_INCLUDE: '(^Snakefile$|.*\.smk$)' # Only include Snakefile and .smk files
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DISABLE_ERRORS: true # TODO: Enforce clean snakefiles in CI
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.pre-commit-config.yaml

@@ -36,7 +36,7 @@ repos:
     hooks:
       - id: snakemake-dryrun
         name: Snakemake Dry Run
-        entry: bash -c 'cd workflow && snakemake -n'
+        entry: bash -c 'cd workflow && poetry run snakemake -n'
         language: system
         files: (Snakefile|\.smk$)
         pass_filenames: false

workflow/Snakefile

@@ -1,16 +1,16 @@
-"""Snakemake file defining the workflows"""
+"""Snakemake file defining the workflows
+"""
+
 
 configfile: "../config/config.yaml"
 
+
 include: "rules/base_coverage.smk"
 include: "rules/amplicon_cov.smk"
-
 # example workflow for testing unit tests
 include: "rules/smk_testing.smk"
 
-conda:
-        "../environment.yml"
 
 rule all:
     input:
-        "../results/statistics.csv"
+        "../results/statistics.csv",