Workflow Name¶
Quick Facts¶
Use the following render_tsv_table macro call that is provided in code below to generate the quick facts table, replacing the fields marked with <> with the appropriate values. Please note that the macro result is seen on the web browser, not the macro call itself.
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
Workflow_Name_On_Terra¶
Please provide a description of the workflow in complete sentences.
Workflow Name Diagram
If a workflow diagram is available, add it here. If not, remove this caption admonition. See the page for TheiaCoV for an example.
Inputs¶
Any additional information regarding the inputs, such as suggestions or guidelines should be found before the table. See the page for Snippy_Streamline for an example.
Add your inputs anywhere in the assets/tables/all_inputs.tsv table. If your workflow has the same type of input as a different workflow, check the inputs table to see if that input already exists. If so, add your workflow name to the comma-delimited list for that input in the appropriate column.
Use the following macro call to generate the inputs table. Adjust the fields marked with <> with the appropriate values. Please note that the macro result is seen on the web browser, not the macro call itself.
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
Workflow Tasks¶
Feel free to separate this section into subsections, like "Read QC" and "Alignment" if there are multiple tasks per subsection for easier navigation and readability. See the page for TheiaMeta for an example.
If your workflow uses a task that is modular and can be used in other contexts, please add that information to the docs/common_text directory in a new page (see a template in the /common_text/template_task.md file) and use the following macro call to include it here. Adjust the fields marked with <> with the appropriate values. Please note that the macro result is seen on the web browser, not the macro call itself.
<tool_name>: <brief description>
Provide sufficient information about your task here so that users can understand how to use the task, what actions it performs, and any important considerations or requirements. Use admonitions as appropriate to highlight important information, tips, or technical details.
Be sure any links within this file are written relative to the destination file. For example, if this file is in docs/common_text/ but is being included in docs/workflows/standalone/ and you want to link to a task in docs/assets/figures/, the link should be written as [link_name](../../assets/figures/link_destination.md).
If your task is used slighly differently in different contexts, you can provide conditionals inside of comments.
To include any conditional information in the destination page, add the condition="condition_name" parameter to the include_md macro call on the destination page. Please note that the if: <condition_name> and endif syntax within the markdown comment (<!-- -->) is required for a conditional statement to work.
Here is an example:
<!-- if: <condition_name> -->
Conditional Content
This is content that is only shown if <condition_name> is provided. See the kraken_task.md common_text file for examples on conditional usage.
<!-- endif -->
This section is required for all tasks. If the Software Source Code, Software Documentation, and/or Original Publication(s) fields are not applicable, they may be removed.
| Links | |
|---|---|
| Task | |
| Software Source Code | |
| Software Documentation | |
| Original Publication(s) |
Outputs¶
Add your outputs to the assets/tables/all_outputs.tsv table. Location doesn't matter. If your workflow has the same type of output as a different workflow, check the output table to see if that output already exists. If so, add your workflow name to the comma-delimited list in the appropriate column.
Use the following macro call to generate the outputs table. Adjust the fields marked with <> with the appropriate values. Please note that the macro result is seen on the web browser, not the macro call itself.
| Variable | Type | Description |
|---|---|---|
Any additional information regarding the outputs, such as interpretation suggestions or more details, should be found after the table. See the page for Kraken2 for an example.
References¶
Include this section if applicable.
reference1
reference2