add more nf-core data entities

.github/workflows/main.yml

@@ -12,7 +12,7 @@ jobs:
   test:
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     runs-on: 'ubuntu-latest'
     steps:
     - name: Checkout

repo2rocrate/nextflow.py

@@ -1,4 +1,5 @@
-# Copyright 2022 CRS4.
+# Copyright 2022-2024 CRS4.
+# Copyright 2024 Matthias Hörtenhuber
 #
 # Licensed under the Apache License, Version 2.0 (the "License"); you may not
 # use this file except in compliance with the License. You may obtain a copy
@@ -65,12 +66,16 @@ class NextflowCrateBuilder(CrateBuilder):
         ("conf", "Dataset", "Configuration files"),
         ("docs", "Dataset", "Markdown files for documenting the pipeline"),
         ("docs/images", "Dataset", "Images for the documentation files"),
+        ("docs/usage.md", "File", "Usage documentation"),
+        ("docs/output.md", "File", "Output documentation"),
         ("lib", "Dataset", "Groovy utility functions"),
         ("modules", "Dataset", "Modules used by the pipeline"),
         ("modules/local", "Dataset", "Pipeline-specific modules"),
         ("modules/nf-core", "Dataset", "nf-core modules"),
         ("workflows", "Dataset", "Main pipeline workflows to be executed in main.nf"),
-        ("subworkflows", "Dataset", "Smaller subworkflows"),
+        ("subworkflows", "Dataset", "Subworkflows used by the pipeline"),
+        ("subworkflows/local", "Dataset", "Pipeline-specific subworkflows"),
+        ("subworkflows/nf-core", "Dataset", "nf-core subworkflows"),
         (CONFIG_BASENAME, "File", "Main Nextflow configuration file"),
         ("README.md", "File", "Basic pipeline usage information"),
         ("nextflow_schema.json", "File", "JSON schema for pipeline parameter specification"),
@@ -79,6 +84,10 @@ class NextflowCrateBuilder(CrateBuilder):
         ("CODE_OF_CONDUCT.md", "File", "The nf-core code of conduct"),
         ("CITATIONS.md", "File", "Citations needed when using the pipeline"),
         ("modules.json", "File", "Version information for modules from nf-core/modules"),
+        ('.nf-core.yml', 'File', 'nf-core configuration file, configuring template features and linting rules'),
+        ('.pre-commit-config.yaml', 'File', 'Configuration file for pre-commit hooks'),
+        ('.prettierignore', 'File', 'Ignore file for prettier'),
+        ('.prettierrc', 'File', 'Configuration file for prettier'),
     ]
 
     @property

setup.py

@@ -35,8 +35,8 @@ def get_version():
     description="Generate RO-Crates from workflow repositories",
     long_description=(THIS_DIR / "README.md").read_text(),
     long_description_content_type="text/markdown",
-    author="Simone Leo",
-    author_email="<[email protected]>",
+    author="Simone Leo, Matthias Hörtenhuber",
+    author_email="<[email protected]>, <[email protected]>",
     license="Apache-2.0",
     platforms=["Linux"],
     classifiers=[
@@ -47,7 +47,7 @@ def get_version():
         "Intended Audience :: Science/Research",
     ],
     packages=["repo2rocrate"],
-    python_requires=">=3.6, <4",
+    python_requires=">=3.9, <4",
     install_requires=["click", "pyyaml", "rocrate"],
     entry_points={
         "console_scripts": ["repo2rocrate=repo2rocrate.cli:cli"],

test/test_nextflow.py

@@ -139,7 +139,7 @@ def test_make_crate(data_dir, defaults):
         ("modules/local", "Dataset", "Pipeline-specific modules"),
         ("modules/nf-core", "Dataset", "nf-core modules"),
         ("workflows", "Dataset", "Main pipeline workflows to be executed in main.nf"),
-        ("subworkflows", "Dataset", "Smaller subworkflows"),
+        ("subworkflows", "Dataset", "Subworkflows used by the pipeline"),
     ]
     for relpath, type_, desc in expected_data_entities:
         entity = crate.get(relpath)