Study Workflow

Studies coordinate the path from sample collection to public submission. This page covers the study lifecycle and the key workflow steps.

Study Lifecycle

Created (Draft)
  → Samples assigned
  → Metadata completed
  → Marked ready for submission
  → Pipelines run (optional)
  → Submitted to ENA
  → Published (with accession IDs)

Draft Stage

A newly created study starts in draft state:

• submitted: false
• readyForSubmission: false
• Samples can be added and removed
• Metadata can be edited freely

Ready for Submission

When all metadata is complete, set readyForSubmission: true. This:

• Records a readyAt timestamp
• Signals to the facility that the study is ready for review
• Does not prevent further editing

Submitted

After successful ENA submission:

• submitted: true with submittedAt timestamp
• studyAccessionId is set (e.g., PRJEB...)
• Each sample receives its own accession numbers
• The study becomes read-only for most fields

Test Submission

SeqDesk supports test submissions to the ENA development server:

• testRegisteredAt records when a test submission was made
• Test submissions expire after 24 hours on ENA’s side
• Use test mode to validate everything before production submission

Running Pipelines from a Study

Studies are the launch point for bioinformatics pipelines:

1. Open the study detail page
2. Navigate to the Pipelines tab
3. Select a pipeline (e.g., MAG)
4. Choose which samples to include
5. Configure pipeline parameters
6. Launch the run

The pipeline system automatically generates a samplesheet from the study’s samples and their assigned reads. See Running a Pipeline for details.

Pipeline Results

After a pipeline completes, results are linked back to the study:

• Assemblies — assembled contigs linked to individual samples
• Bins — genome bins with completeness and contamination scores
• Artifacts — QC reports, MultiQC summaries, and other outputs

Results appear in the study’s Pipelines tab and on individual sample pages.

Internal Notes

Studies support internal notes with edit tracking:

• Any user with access can add or edit notes
• The system tracks who edited the notes and when
• Notes are visible on the study overview tab

Deleting a Study

Studies can be deleted if they have not been submitted to ENA:

• Deleting a study unassigns all its samples (sets studyId to null)
• The samples remain in their original orders
• Pipeline runs associated with the study are preserved for reference
• Submitted studies cannot be deleted