From 834a7f25c0a453e4597400e508d1dcd9c7664a74 Mon Sep 17 00:00:00 2001
From: Florian De Temmerman <florian.detemmerman@lizard.bio>
Date: Thu, 29 Feb 2024 22:18:38 +0100
Subject: [PATCH] Reformat and fix linting errors

---
 .pre-commit-config.yaml                       | 27 ++++++++++---------
 assets/nf-params.yml                          |  8 +++---
 bin/collect_metadata.py                       |  8 ++++--
 .../templates/dumpsoftwareversions.py         |  4 ++-
 4 files changed, 29 insertions(+), 18 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index bce64572..801e349a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,4 +1,18 @@
+exclude: ^(.*.test.snap)|(assets/nf-params.yml)$
+
 repos:
+  - repo: local
+    hooks:
+      - id: nf-core/tools parameters.yaml
+        name: Update nf-params.yml file with schema
+        language: python
+        additional_dependencies:
+          - nf-core
+        entry: nf-core
+        args: [create-params-file, --output, assets/nf-params.yml, "--force", "."]
+        pass_filenames: false
+        files: ^nextflow_schema.json$
+
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"
     hooks:
@@ -8,20 +22,9 @@ repos:
     hooks:
       - id: editorconfig-checker
         alias: ec
+        exclude: assets/nf-params.yml
 
   - repo: https://github.com/psf/black
     rev: 23.3.0
     hooks:
       - id: black
-
-  - repo: local
-    hooks:
-      - id: nf-core/tools parameters.yaml
-        name: Update nf-params.yml file with schema
-        language: python
-        additional_dependencies:
-          - nf-core
-        entry: nf-core
-        args: [create-params-file, --output, assets/nf-params.yml, "--force", "."]
-        pass_filenames: false
-        files: ^nextflow_schema.json$
diff --git a/assets/nf-params.yml b/assets/nf-params.yml
index 4816169f..5e6c9928 100644
--- a/assets/nf-params.yml
+++ b/assets/nf-params.yml
@@ -1,5 +1,5 @@
 ## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-##     nf-core/pixelator 1.0.3
+##     nf-core/pixelator 1.1.0dev
 ## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ##     This is an example parameter file to pass to the `-params-file` option
 ##     of nextflow run with the nf-core/pixelator pipeline.
@@ -19,6 +19,7 @@
 ##     Path to comma-separated file containing information about the samples
 ##     in the experiment.
 ##     Type: string
+##     Required
 ## -----------------------------------------------------------------------------
 # input = null
 
@@ -37,8 +38,9 @@
 ##     The output directory where the results will be saved. You have to use
 ##     absolute paths to storage on Cloud infrastructure.
 ##     Type: string
+##     Required
 ## -----------------------------------------------------------------------------
-# outdir = "./results"
+# outdir = null
 
 ## -----------------------------------------------------------------------------
 ## email
@@ -404,7 +406,7 @@
 ## =============================================================================
 ## Less common options for the pipeline, typically set in a config file.
 
-## (12 hidden parameters are not shown)
+## (11 hidden parameters are not shown)
 
 
 
diff --git a/bin/collect_metadata.py b/bin/collect_metadata.py
index 67df83b7..8eef3d74 100755
--- a/bin/collect_metadata.py
+++ b/bin/collect_metadata.py
@@ -20,7 +20,9 @@
 
 
 def subtool_versions():
-    cutadapt_proc = subprocess.run(["cutadapt", "--version"], capture_output=True, text=True)
+    cutadapt_proc = subprocess.run(
+        ["cutadapt", "--version"], capture_output=True, text=True
+    )
     fastp_proc = subprocess.run(["fastp", "--version"], capture_output=True, text=True)
 
     cutadapt_version = cutadapt_proc.stdout.strip("\n")
@@ -73,7 +75,9 @@ def main(args):
     parser = argparse.ArgumentParser()
 
     parser.add_argument("--process-name", dest="process_name", type=str)
-    parser.add_argument("--workflow-data", dest="workflow_data", type=Path, default=None)
+    parser.add_argument(
+        "--workflow-data", dest="workflow_data", type=Path, default=None
+    )
     args = parser.parse_args()
 
     main(args)
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index da033408..4a993608 100755
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -58,7 +58,9 @@ def main():
     }
 
     with open("$versions") as f:
-        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+        versions_by_process = (
+            yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+        )
 
     # aggregate versions by the module name (derived from fully-qualified process name)
     versions_by_module = {}