From e60b236885c16e5ca6607fc17b0ecfa2688e91df Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 17 Oct 2024 17:18:36 +0200 Subject: [PATCH 1/6] add more nf-core data entities --- repo2rocrate/nextflow.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/repo2rocrate/nextflow.py b/repo2rocrate/nextflow.py index 7a20b67..cdb936b 100644 --- a/repo2rocrate/nextflow.py +++ b/repo2rocrate/nextflow.py @@ -65,12 +65,16 @@ 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"), + ("suborkflows/local", "Dataset", "Pipeline-specific suborkflows"), + ("suborkflows/nf-core", "Dataset", "nf-core suborkflows"), (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 +83,10 @@ 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 From 66ee243fcbc476e6ec63cb2122250bb2e22765a0 Mon Sep 17 00:00:00 2001 From: simleo Date: Fri, 18 Oct 2024 16:00:51 +0200 Subject: [PATCH 2/6] fix typo --- repo2rocrate/nextflow.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2rocrate/nextflow.py b/repo2rocrate/nextflow.py index cdb936b..71d6ca1 100644 --- a/repo2rocrate/nextflow.py +++ b/repo2rocrate/nextflow.py @@ -1,4 +1,4 @@ -# Copyright 2022 CRS4. +# Copyright 2022-2024 CRS4. # # 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 @@ -73,8 +73,8 @@ class NextflowCrateBuilder(CrateBuilder): ("modules/nf-core", "Dataset", "nf-core modules"), ("workflows", "Dataset", "Main pipeline workflows to be executed in main.nf"), ("subworkflows", "Dataset", "Subworkflows used by the pipeline"), - ("suborkflows/local", "Dataset", "Pipeline-specific suborkflows"), - ("suborkflows/nf-core", "Dataset", "nf-core suborkflows"), + ("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"), From fc16c46bc2a4be3931abf3f5560c745b26f27b8a Mon Sep 17 00:00:00 2001 From: simleo Date: Fri, 18 Oct 2024 16:11:39 +0200 Subject: [PATCH 3/6] update nextflow test --- test/test_nextflow.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/test_nextflow.py b/test/test_nextflow.py index be8f0a0..afa1b9a 100644 --- a/test/test_nextflow.py +++ b/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) From 3feb20d670559e1df8ac03d26d60c6e22534d025 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 23 Oct 2024 12:24:50 +0200 Subject: [PATCH 4/6] add myself to author list --- setup.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/setup.py b/setup.py index 71ab7ae..69cf0eb 100644 --- a/setup.py +++ b/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="", + author="Simone Leo, Matthias Hörtenhuber", + author_email=", ", 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=">=3.8, <4", install_requires=["click", "pyyaml", "rocrate"], entry_points={ "console_scripts": ["repo2rocrate=repo2rocrate.cli:cli"], From 03945c8153af5c153354b1f9bc3295b428e8aee5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Thu, 31 Oct 2024 08:37:35 +0000 Subject: [PATCH 5/6] add copyright statement --- repo2rocrate/nextflow.py | 1 + 1 file changed, 1 insertion(+) diff --git a/repo2rocrate/nextflow.py b/repo2rocrate/nextflow.py index 71d6ca1..5e3f46a 100644 --- a/repo2rocrate/nextflow.py +++ b/repo2rocrate/nextflow.py @@ -1,4 +1,5 @@ # 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 From 17f1d0c0bde4aacdbe442916618b730d355f3a60 Mon Sep 17 00:00:00 2001 From: simleo Date: Tue, 5 Nov 2024 11:22:05 +0100 Subject: [PATCH 6/6] bump min required python version --- .github/workflows/main.yml | 2 +- setup.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 7aa44f6..9611aa4 100644 --- a/.github/workflows/main.yml +++ b/.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 diff --git a/setup.py b/setup.py index 69cf0eb..9b93799 100644 --- a/setup.py +++ b/setup.py @@ -47,7 +47,7 @@ def get_version(): "Intended Audience :: Science/Research", ], packages=["repo2rocrate"], - python_requires=">=3.8, <4", + python_requires=">=3.9, <4", install_requires=["click", "pyyaml", "rocrate"], entry_points={ "console_scripts": ["repo2rocrate=repo2rocrate.cli:cli"],