• Form Bio Reserved Nextflow Configuration values
• Form Bio Reserved Nextflow Param values
• Source code repository requirements
• Create correct structure
• Convert json schema
• Update nextflow.config
• Import Workflow
• Importing a new or existing workflow
• Monitor
• Workflow JSON schema
• Inputs
• Field Inputs
• UI

Form Bio Reserved Nextflow Configuration values

The following configuration is provided by the Form Bio platform at workflow runtime, and will be ignored if set by the workflow via nextflow.config or in main.nf.

See Nextflow Configuration documentation

Configuration — Nextflow 23.10.0 documentation

Introduction

www.nextflow.io

Form Bio Reserved Nextflow Param values

The following params are reserved and provided by the Form Bio platform and will be overwritten if provided by the workflow or as user-provided input params.

Source code repository requirements

Create correct structure

1. Ensure main.nf and nextflow.config live in the root of the repo.
2. Create a “workflows” directory inside the repo, if one does not already exist.
3. Inside that directory, create another directory with same name as the ID of the workflow (if one does not already exist).
4. Inside that directory, create a workflow.json file (the GUI input specification) and optional documentation files: overview.md citations.md inputs.md ,outputs.md .
1. You can symlink any documentation that already exists in the repo here under the above names, or create these docs from scratch.
2. The workflow.json schema is covered in detail below.

Convert json schema

Convert the repo’s existing json schema to a Form Bio workflow schema in workflow.json, using our Workflow JSON Schema Guide (below) to help you.

Update nextflow.config

Beneath the section where default params are defined, include statement that remaps our output param to theirs:

params.out_dir = "${params.output}" where “out_dir” is their param name

Import Workflow

Our GitHub app allows for fast, observable automation driven by pushes to workflow repositories on GitHub. Once a workflow is imported, any push to that repo will trigger an upload of the workflow under the version of the branch pushed to.

Importing a new or existing workflow

1. Inside the Form Bio web app, navigate to the Manage section under Workflows.
2. Select Create New.
3. If you have not linked your GitHub account to the FormBio GitHub App yet, please click Sign in with GitHub and Authorize access.
4. Once authorized, you will be redirected to the Web App and see an Import Workflow from GitHub screen.
5. Select formbio under Select Account.
6. Select the repository containing the workflow you would like to import under Select Repository
1. If you do not see the repository you are looking for you will need to install the App to it
2. To do this, open up the Select Account dropdown again and select Add or Modify Installations
3. From there, select formbio organization and select the repositories you would like to install the app onto.
4. Click Update Access
5. You will be redirected back to the Web App where you can now select that repository
7. The Select Workflow list should automatically detect the workflows located within the repo’s workflows/ directory that contain a workflow.json for you.
8. Click Configure on the workflow you’d like to import.
9. The configure form should be pre-populated with the default values and paths. It is strongly discouraged to change any of these at this time.
10. Click Import Workflow and you’ll be redirected to the main branch’s build in progress. (See below, Monitor step 6).

Monitor

1. Inside the Form Bio web app, navigate to the Manage section under Workflows (See first step in Import).
2. You’ll see a list of cards representing all workflows that have been uploaded to the current project (whether via CLI or GitHub App) listed here.
3. Workflows imported via GitHub App will be indicated by a GH logo and a View Deployments button.
4. Click View Deployments to see a record of all uploads since being imported. To see logs for a particular upload, click View Logs.
5. You’ll be taken to a logs view, displaying data about the workflow, version, and build status.
6. If an upload was successful, you’ll see a Go to Launch button that will take you to the docs page for that version, where you can Launch the workflow.

Workflow JSON schema

Form Bio schemas currently support the configuration of workflows as JSON. They define metadata for the workflow, the necessary and optional parameters needed for a successful run, how those parameters should be presented in forms in the web application, as well as conditionals that allow the schema to dynamically respond to certain input values being provided by users.

Here is a simple example schema:

{
	"id": "myWorkflowSchema",
	"schema": "v3",
	"displayName": "My Workflow Schema",
	"description": "Here is my workflow schema",
	"title": "formbio/nf-myWorkflow",
	"workflowVersion": "v1.0.0",
	"categories": ["My Workflow Category"],
	"inputs": {
		"myFirstTextInput": {
			"title": "My First Text Input",
			"type": "string",
			"hidden": false,
			"required": true,
			"description": "Here is a description",
			"help_text": "Here are more details....",
			"default": "my default value",
			"pattern": "someRegexPatternItMustMatch"
		},
		"mySecondTextInput": {
			"title": "My Second Text Input",
			"type": "string",
			"hidden": false,
			"required": true,
			"description": "Here is a description",
			"help_text": "Here are more details....",
			"default": "my default value",
			"pattern": "someRegexPatternItMustMatch"
		}
	},
	"ui": {
		"inputs": [
			{
				"id": "myGroup",
			  "title": "My Group",
				"fields": ["myFirstTextInput", "mySecondTextInput"],
			  "help_text": "More information on this grouping...",
			  "description": "Here is a description",
			  "hidden": false
			}
		]
	},
}

Inputs

Field Inputs

Field inputs represent a run parameter whose value can be provided by a user. The Field Input configuration defines the type of input to display in the form in the web application, as well as labels, help texts, default values, and various forms of validation, depending on the field.

Every Field Input contains the following properties: title, hidden, required, description, and help_text

• description should be a concise description of parameter as it will be displayed immediately below the input in the form. These can be dynamically updated using conditionals.
• help_text can be more verbose explanations of the parameters as these will be displayed in a collapsable help drawer to the right of the form. These cannot be dynamically updated using conditionals, so it maybe helpful to provide insight here as to why an input might change.

UI