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{{ title }}
{% if pipeline.metadata.description %}{{ pipeline.metadata.description|markdown }}
{% endif %} {% if pipeline.metadata.homepage or pipeline.metadata.repository %}
{% if pipeline.metadata.homepage %}
{{ pipeline.metadata.homepage }}
{% endif %} {% if pipeline.metadata.repository and pipeline.metadata.repository !=
pipeline.metadata.homepage %}
{% if 'github.com' in pipeline.metadata.repository %}
{% else %}
{% endif %} {{ pipeline.metadata.repository }}
{% endif %}
{% endif %} {% if pipeline.metadata.readme_content %}
{{ pipeline.metadata.readme_content|markdown_with_anchors }}
{% endif %} {% if pipeline.metadata.authors %}
Authors
-
{% for author in pipeline.metadata.authors %}
- {{ author }} {% endfor %}
Pipeline Inputs
This page documents all input parameters for the pipeline.
{% for group, items in input_groups.items() %}{{ group }} ¶
{% for inp in items %}
--{{ inp.name }}
¶
{{ inp.type }}
{% if inp.format %}
{{ inp.format }}
{% endif %} {% if inp.pattern %}
Pattern:
{% if inp.description %}
{{ inp.pattern }}
{% endif %} {% if inp.required %}
Required
{% else %}
Optional
{% endif %}
{{ inp.description|markdown }}
{% endif %} {% if inp.help_text %}
{{ inp.help_text|markdown }}
{% endif %} {% if inp.default is not none %}
Default:
{{ inp.default }}
Allowed values:
{% for val in inp.enum %}
{{ val }}
{% if not loop.last %}, {% endif %} {% endfor %}
Configuration Parameters
These are additional configuration parameters that are not primary pipeline inputs.
{% for param in pipeline.config_params %}
{{ param.name }}
¶
{{ param.type }}
{% if param.description %}
{{ param.description|markdown }}
{% endif %} {% if param.default is not none %}
Default:
{{ param.default }}
Workflows
This page documents all workflows in the pipeline.
{% for wf in pipeline.workflows|sort(attribute='name') %}
workflow
{{ wf.name or '<entry>' }}
{% if wf.is_entry %}
Entry Point
{% endif %} {% if wf.source_url %}
[source]
{% endif %}
¶
{% if wf.file %}
Defined in
{% endif %}
{% if wf.meta_keywords %}
{{ wf.file }}:{{ wf.line }}
{% for keyword in wf.meta_keywords %}
{{ keyword }}
{% endfor %}
{% endif %}
{% if wf.meta_description %}
{{ wf.meta_description|markdown }}
{% endif %}
{% if wf.docstring and wf.docstring != wf.meta_description %} {% if wf.meta_description
%}
Code Documentation
{% endif %}{{ wf.docstring|markdown }}
{% endif %}
{% if wf.meta_components %}
Components
{% for comp in wf.meta_components %}
{% endif %}
{% if wf.inputs or wf.meta_inputs %}
{{ comp|wbr }}
{% endfor %}
Inputs (take)
| Name | Description |
|---|---|
{{ inp.name|wbr }}
|
{% if inp.description %}
{{ inp.description|markdown }}
{% else %}-{% endif %}
|
{{ inp.name|wbr }}
|
{% if inp.description %}
{{ inp.description|markdown }}
{% else %}-{% endif %}
|
Outputs (emit)
| Name | Description |
|---|---|
{{ out.name|wbr }}
|
{% if out.description %}
{{ out.description|markdown }}
{% else %}-{% endif %}
|
{{ out.name|wbr }}
|
{% if out.description %}
{{ out.description|markdown }}
{% else %}-{% endif %}
|
Calls
-
{% for call in wf.calls %}
-
{{ call|wbr }}
{% endfor %}
{% if wf.meta_authors %}
Authors:
{% for author in wf.meta_authors %} {%- if author.startswith('@') -%}
{{ author }}
{%- else -%} {{ author }} {%- endif -%} {%- if not loop.last %}, {% endif -%} {%
endfor %}
{% endif %} {% if wf.meta_maintainers %}
Maintainers:
{% for maintainer in wf.meta_maintainers %} {%- if maintainer.startswith('@') -%}
{{ maintainer }}
{%- else -%} {{ maintainer }} {%- endif -%} {%- if not loop.last %}, {% endif -%} {%
endfor %}
{% endif %}
{% endif %}
Processes
This page documents all processes in the pipeline.
{% for proc in pipeline.processes|sort(attribute='name') %}
process
{{ proc.name }}
{% if proc.source_url %}
[source]
{% endif %} {% if proc.nfcore_module_url %}
{% endif %}
¶
{% if proc.file %}
Defined in
{% endif %}
{% if proc.meta_keywords %}
{{ proc.file }}:{{ proc.line }}
{% for keyword in proc.meta_keywords %}
{{ keyword }}
{% endfor %}
{% endif %}
{% if proc.meta_description %}
{{ proc.meta_description|markdown }}
{% endif %}
{% if proc.docstring and proc.docstring != proc.meta_description %} {% if
proc.meta_description %}
Code Documentation
{% endif %}{{ proc.docstring|markdown }}
{% endif %}
{% if proc.meta_tools %}
Tools
{% for tool in proc.meta_tools %}
{% if tool.homepage %}
{{ tool.name }}
{% elif tool.documentation %}
{{ tool.name }}
{% else %} {{ tool.name }} {% endif %}
{% if tool.description %}
{{ tool.description|markdown }}
{% endif %}
{% if tool.homepage %}
Homepage
{% endif %} {% if tool.documentation %}
Documentation
{% endif %} {% if tool.identifier and tool.identifier.startswith('biotools:') %}
{{ tool.identifier }}
{% elif tool.identifier %}
{{ tool.identifier }}
{% endif %} {% if tool.licence %}
License: {{ tool.licence|join(', ') }}
{% endif %}
Inputs
| Name | Type | Description |
|---|---|---|
{{ inp.name|wbr }}
|
{{ (inp.type or '-')|wbr }}
|
{% if inp.description %}
{{ inp.description|markdown }}
{% else %}-{% endif %}
|
{{ inp.name|wbr }}
|
{{ inp.type|wbr }}
|
{% if inp.description %}
{{ inp.description|markdown }}
{% else %}-{% endif %}
|
Outputs
| Name | Type | {% if not proc.meta_outputs %}Emit{% else %}Pattern{% endif %} | Description |
|---|---|---|---|
{{ out.name|wbr }}
|
{{ (out.type or '-')|wbr }}
|
{% if out.pattern %}
{{ out.pattern|wbr }}
{% else %}-{% endif %}
|
{% if out.description %}
{{ out.description|markdown }}
{% else %}-{% endif %}
|
{{ out.name|wbr }}
|
{{ out.type|wbr }}
|
{% if out.emit %}
{{ out.emit|wbr }}
{% else %}-{% endif %}
|
{% if out.description %}
{{ out.description|markdown }}
{% else %}-{% endif %}
|
Directives
| Directive | Value |
|---|---|
{{ name|wbr }}
|
{{ value|wbr }}
|
{% if proc.meta_authors %}
Authors:
{% for author in proc.meta_authors %} {%- if author.startswith('@') -%}
{{ author }}
{%- else -%} {{ author }} {%- endif -%} {%- if not loop.last %}, {% endif -%} {%
endfor %}
{% endif %} {% if proc.meta_maintainers %}
Maintainers:
{% for maintainer in proc.meta_maintainers %} {%- if maintainer.startswith('@') -%}
{{ maintainer }}
{%- else -%} {{ maintainer }} {%- endif -%} {%- if not loop.last %}, {% endif -%} {%
endfor %}
{% endif %}
{% endif %}
Functions
This page documents helper functions defined in the pipeline.
{% for func in pipeline.functions|sort(attribute='name') %}
def
{{ func.name }}({% for p in func.params %}{{ p.name }}{% if not loop.last %}, {% endif %}{% endfor
%}) {% if func.source_url %}
[source]
{% endif %}
¶
{% if func.file %}
Defined in
{% endif %} {% if func.docstring %}
{{ func.file }}:{{ func.line }}
{{ func.docstring|markdown }}
{% endif %} {% if func.params %}
Parameters
| Name | Description | Default |
|---|---|---|
{{ p.name|wbr }}
|
{% if p.description %}
{{ p.description|markdown }}
{% else %}-{% endif %}
|
{% if p.default is not none %}
{{ p.default|wbr }}
{% else %}-{% endif %}
|
Returns
{{ func.return_description }}
{% endif %}