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Sample Sheets ​

Sample sheets are the metadata templates used to define inputs for your bioinformatic pipelines. They bridge the gap between your raw data and executable workflows by mapping sample IDs to specific file paths and experimental parameters.

Creating a Sample Sheet ​

To create a new sheet, click New sample sheet. While you can create a generic sheet, the platform is optimized for structured workflows:

  • Workflow Association: You can optionally select a specific workflow and version.
  • Auto-Schema Generation: When a workflow is selected, the platform automatically generates the required column headers and validation rules based on that pipeline's specific requirements.

Current Limitations

Support for interactive sample sheets is currently focused on the nf-core suite. While other workflow types can be selected, the automated schema generation and validation are primarily tailored for nf-core standards.

Populating Data ​

Once a sample sheet is created, you can populate it with data from your project.

Importing from Cohorts ​

For supported pipelines, the most efficient way to fill your sheet is by using the Import from Cohort utility:

  • Automated Mapping: Select a cohort that contains the samples you need. The platform will automatically resolve the S3 file paths for the samples and populate the data columns.
  • File Type Support: This automated population currently only supports FASTQ file types within nf-core workflow schemas.

Manual Entry and Validation ​

You can interactively edit the cells within the sample sheet interface:

  • Dropdown Selection: For specific columns like strandedness, the editor provides pre-defined options (e.g., forward, reverse, unstranded, auto) to ensure data consistency.
  • Validation: Click the Validate button to check your sheet against the workflow's schema. The platform will highlight errors in red, such as missing files or invalid parameters, ensuring your workflow run doesn't fail due to formatting issues.

Management and Alternatives ​

The sample sheet view includes standard management tools to Save, Edit (rename), or Delete the asset.

TIP

If you have a complex or pre-existing sample sheet that does not fit the current interactive templates, you can always upload it as a standalone file within a Dataset.


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