2.1 Registering an Account

1. Open CASSIE in your web browser.
2. Click "Register" or "Sign Up" on the landing page.
3. Fill in your name, email address, and choose a password.
4. Check your inbox for a verification email and click the confirmation link.
5. After verification, you will be redirected to the login page.

2.2 Logging In

1. Go to the CASSIE login page.
2. Enter your registered email and password.
3. Click "Log In" to open the Home dashboard.
4. If you forget your password, use the "Forgot Password" link on the login page to request a reset email.

2.3 Navigating the Interface

The main navigation bar runs across the top of the application. Depending on whether you are signed in, you will typically see the following links and controls:

• Home: Your dashboard and main starting point.
• Jobs: History of all jobs you have run.
• Pipelines: Manage your saved workflows and starter templates.
• Storage: Manage uploaded inputs and generated outputs after signing in.
• Community: Browse shared pipelines published by other users.
• Forum: Read and create discussion threads.
• Balance: Review available and reserved funds for job execution.
• Account Menu: Open your profile and account actions.

The Home page also provides shortcut cards for viewing jobs, opening pipelines, creating a job, and launching the pipeline builder.

3.1 Uploading Files

1. Click "Storage" in the navigation menu.
2. Select the Input Files tab if it is not already active.
3. Click "Upload from Computer" to choose local files, or use the Google Drive import option if it is configured.
4. Select one or more files from your computer.
5. Wait for the upload queue to finish and for the files to appear in the storage library.
6. Confirm that the uploaded file appears in your input file list.

3.2 Supported File Formats

CASSIE recognizes the following common genomic and workflow-related file formats:

• FASTQ (.fastq, .fq, .fastq.gz): Short-read sequencing data.
• FASTA (.fasta, .fa, .fna): Reference sequences.
• GFF (.gff, .gff3): Genome annotations.
• Additional supported formats include .gtf, .hal, .gfa, .csv, .tsv, .json, and .txt, including supported compressed variants.

If CASSIE does not automatically detect a file format, you can set it manually using the override format option next to the file.

4.1 Creating a One-off Job

1. Open the Create Job flow from the Home page shortcut or from a pipeline action such as "Use in Job".
2. Select the desired bioinformatics tool from the tool dropdown.
3. Under input files, add the file or files required by the selected tool.
4. Review the estimated runtime and cost shown on the page.
5. Click "Submit Job" to queue the job for execution.

4.2 Configuring Tool Parameters

Most tools expose optional parameters below the file picker. Common examples include genome size, coverage depth, or output format flags. Hover over parameter labels to view short descriptions. Leave fields blank to use the default tool settings.

4.3 Monitoring Job Progress

1. Open the "Jobs" page from the navigation menu.
2. Click a job row to open its detail view.
3. Review the current status, the stage-by-stage progress indicator, and the live log output.
4. If a job fails, review the error summary and use the retry option if available.

4.4 Downloading Results

1. Once the job reaches Completed status, scroll to the outputs section.
2. Download files one by one or use the "Download All" option to retrieve everything as a ZIP archive.

5.1 Creating a New Pipeline

1. Open the builder from the Home page shortcut or from the Pipelines page using "Create New Pipeline".
2. If no pipeline is open yet, start with a blank pipeline canvas.
3. Enter a name for the new pipeline when prompted.

5.2 Adding and Connecting Nodes

The builder canvas supports several node types:

• Input: Represents an uploaded file from Storage.
• Tool: A bioinformatics processing step.
• Checkpoint: A pause point for manual review.
• Result: Marks the final output of the pipeline.

To build a pipeline, add an input node, place a tool node beside it, connect output handles to input handles, continue linking tools in sequence, and finish with a result node.

5.3 Saving and Naming Pipelines

1. Click the Save button in the toolbar whenever you want to preserve your work.
2. Rename a pipeline by editing the title shown at the top of the builder.
3. Clone an existing pipeline through the pipeline menu if you want to reuse and modify it.

5.4 Running a Pipeline Job

1. Open an existing pipeline in the builder or from your Pipelines page.
2. Click "Run Pipeline".
3. Map each input node to a file from Storage.
4. Submit the pipeline run and verify that it appears in your Jobs list.

5.5 Publishing a Pipeline to the Community

1. Open the Pipelines page to see your saved pipelines.
2. Find the pipeline you want to share and use the Share action on its card.
3. After sharing, the pipeline is marked as Shared in your own pipeline list.
4. Open the Community page to confirm that the shared pipeline is visible to other users.