Added pyproject.toml

.github/workflows/test.yml

@@ -50,7 +50,7 @@ jobs:
             main.nf \
             -profile local,docker \
             -stub \
-            -params-file tests/stub/test_stub.json
+            -params-file tests/stub/params.json
 
   confirm-pass:
     runs-on: ubuntu-latest

CHANGELOG.md

@@ -47,6 +47,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 38. Updated `pfr_pangene` and `pfr/profile.config`
 39. Now using local tests/stub files for GitHub CI
 40. Now removing iso-forms left by TSEBRA using `AGAT_SPFILTERFEATUREFROMKILLLIST`
+41. Added `pyproject.toml`
 
 ### `Fixed`
 

local_pangene

@@ -17,6 +17,5 @@ nextflow run \
     -profile local,docker \
     -resume \
     $stub \
-    -params-file pangene-test/test_params.json \
-    --eggnogmapper_db_dir ../../dbs/emapperdb/5.0.2 \
-    --eggnogmapper_tax_scope 33090
+    -params-file pangene-test/params.json \
+    --eggnogmapper_db_dir ../dbs/emapperdb/5.0.2

pyproject.toml

@@ -0,0 +1,15 @@
+# Config file for Python. Mostly used to configure linting of bin/*.py with Ruff.
+# Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
+[tool.ruff]
+line-length = 120
+target-version = "py38"
+cache-dir = "~/.cache/ruff"
+
+[tool.ruff.lint]
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+
+[tool.ruff.lint.isort]
+known-first-party = ["nf_core"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]

tests/stub/test_stub.json → tests/stub/params.json

@@ -1,7 +1,8 @@
 {
     "input": "tests/stub/assemblysheet.csv",
-    "eggnogmapper_db_dir": "tests/stub/emapperdb/5.0.2",
     "external_protein_fastas": "tests/stub/external-protein-fastas.txt",
+    "eggnogmapper_db_dir": "tests/stub/emapperdb/5.0.2",
+    "eggnogmapper_tax_scope": 33090,
     "fastq": "tests/stub/fastqsheet.csv",
     "liftoff_annotations": "tests/stub/liftoffannotations.csv",
     "max_cpus": 2,