diff --git a/README.md b/README.md index fff86fb3ed3dcef530d4ceeb886c340e8edd49bc..422a9100f9948a903afbd38f42b2dd7941e67032 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [](https://www.gnu.org/licenses/gpl-3.0) -[]() +[]() ## Description @@ -125,7 +125,7 @@ The structure of this folder is organised as such : └── ro-crate-metadata-rnaseq-nf.json ``` -* The `ro-crate-metadata-rnaseq-nf.json` describes the workflow following an extended Workflow [RO-Crate](https://www.researchobject.org/ro-crate/) profile. The description of this extended profile can be found [here]() (TODO) +* The `ro-crate-metadata-rnaseq-nf.json` describes the workflow following an extended Workflow [RO-Crate](https://www.researchobject.org/ro-crate/) profile. The description of this extended profile can be found [here](https://gitlab.liris.cnrs.fr/sharefair/posters/swat4hcls-2024). * the `debug` folder contains different intermediary files which are ussefull for debugging * the `graphs` folder contains the different graphs which are generated. For each of the 3 graphs described above, **BioFlow-Insight** generates : * A `json` file which describes the graph using **BioFlow-Insight** specific format diff --git a/bioflow_insight_cli/main.py b/bioflow_insight_cli/main.py index 1e0357e2067f1165c64976305379f8d947d22faa..f622c794b9e190977a5dc89d38c51347d79e169b 100644 --- a/bioflow_insight_cli/main.py +++ b/bioflow_insight_cli/main.py @@ -8,7 +8,7 @@ from src.workflow import Workflow @click.version_option(bioflow_insight_src.__version__) @click.argument('main_workflow_path') #@click.option('--author', 'author', required=False, help='Author name, extracted otherwise') -@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise') +@click.option('--name', 'name', required=False, help='Workflow name, extracted otherwise (in the case of a Git repo)') @click.option('--output-dir', default='./results', help='Where the results will be written') @click.option( '--no-duplicate', diff --git a/pyproject.toml b/pyproject.toml index e1c078858640d730904952bd31001cda2646f46c..08b4297bb169131c0db64432e52cce6124cde6f0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta" [project] name = "bioflow-insight" authors = [ - { name="George Marchment", email="author@example.com" }, + { name="George Marchment"}, ] description = "A software to extract and analyze the structure and associated metadata from a Nextflow workflow." readme = "README.md" @@ -26,8 +26,8 @@ version = {attr = "src.__version__"} bioflow-insight = "bioflow_insight_cli.main:cli_command" [project.urls] -Homepage = "https://github.com/George-Marchment/Newtflow-Structure" -Issues = "https://github.com/George-Marchment/Newtflow-Structure/issues" +Homepage = "https://gitlab.liris.cnrs.fr/sharefair/bioflow-insight" +Issues = "https://gitlab.liris.cnrs.fr/sharefair/bioflow-insight/-/issues" [tool.setuptools] packages = [