YAML to Markdown

• YAML to Markdown
  • requirements
  • usage
    • validate yaml
    • convert yaml for modules
    • convert yaml for sub-workflows
    • validate and convert yaml modules
    • validate and convert yaml sub-workflows
  • validate
  • convert
  • all
  • read_yaml
  • convert_yaml_to_markdown_modules
  • convert_yaml_to_markdown_subworkflows

requirements

• python==3.10
• jsonschema==4.21.1
• requests==2.31.0
• typer==0.9.0
• PyYaml==6.0.1

usage

validate yaml

python yaml_to_md.py validate -y test.yaml

convert yaml for modules

python yaml_to_md.py convert -y test.yaml

convert yaml for sub-workflows

python yaml_to_md.py convert -y test.yaml -S

validate and convert yaml modules

python yaml_to_md.py all -y test.yaml

validate and convert yaml sub-workflows

python yaml_to_md.py all -y test.yaml -S

validate

The validate function validates a YAML data against a JSON schema retrieved from a given URL.

Arguments:

• yaml_file (Path): The yaml_file parameter is the path to the YAML file that you want to convert to Markdown. It is specified using the --yaml-file or -y option when running the script. The file should exist and be readable
• schema_url: The schema_url parameter is a URL that points to a JSON schema file. This schema file defines the structure and validation rules for the YAML data

convert

The convert function is a Python script that converts a YAML file into a Markdown file.

Arguments:

• yaml_file (Path): The yaml_file parameter is the path to the YAML file that you want to convert to Markdown. It is specified using the --yaml-file or -y option when running the script. The file should exist and be readable
• subworkflows (Annotated[ Optional[bool], typer.Option("--subworkflows/--modules", "-S/-m")] (optional)): The subworkflows parameter is a boolean flag that determines whether to convert the YAML file to Markdown using subworkflows or modules. It is specified using the --subworkflows or -S option when running the script. If the flag is provided, the YAML file will be, defaults to False
• output_file (str): The output_file parameter is the path to the output Markdown file. It specifies the file where the converted Markdown content will be saved. By default, the value is set to "output.md". However, you can provide a different file path if desired

all

The all function is a Python script that validates and converts a YAML file into a Markdown file based on a specified JSON schema.

Arguments:

• yaml_file (Path): The yaml_file parameter is the path to the YAML file that you want to convert to Markdown. It is specified using the --yaml-file or -y option when running the script. The file should exist and be readable
• subworkflows (Annotated[ Optional[bool], typer.Option("--subworkflows/--modules", "-S/-m")] (optional)): The subworkflows parameter is a boolean flag that determines whether to convert the YAML file to Markdown using subworkflows or modules. It is specified using the --subworkflows or -S option when running the script. If the flag is provided, the YAML file will be, defaults to False
• schema_url (str): The schema_url parameter is the URL of the JSON schema that will be used to validate the YAML data. In this code, the default value for schema_url is set to "https://raw.githubusercontent.com/mskcc-omics-workflows/yaml_to_md/main/nextflow_schema/meta-schema.json" derived from "https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json". However, you can provide one as well
• output_file (str): The output_file parameter is the path to the output Markdown file. It specifies the file where the converted Markdown content will be saved. By default, the value is set to "output.md". However, you can provide a different file path if desired

read_yaml

def read_yaml(yaml_file)

The function read_yaml reads the contents of a YAML file and returns it as a string.

Arguments:

• yaml_file: The yaml_file parameter is a file object that represents a YAML file

Returns:

the contents of the YAML file as a string.

convert_yaml_to_markdown_modules

def convert_yaml_to_markdown_modules(data)

The convert_yaml_to_markdown_modules function takes in a YAML data structure and converts it into a Markdown format.

Arguments:

• data: The data parameter is a dictionary that contains information about a module.

Returns:

a Markdown-formatted string that contains information about a module. The string includes the module's name, description, keywords, tools, inputs, outputs, authors, and maintainers.

convert_yaml_to_markdown_subworkflows

def convert_yaml_to_markdown_subworkflows(data)

The convert_yaml_to_markdown_subworkflows function takes in a YAML data structure and converts it into a Markdown format.

Arguments:

• data: The data parameter is a dictionary that contains information about a module.

Returns:

a Markdown-formatted string that contains information about a module. The string includes the module's name, description, keywords, components, inputs, outputs, and authors.