ENA Reads and Assembly Submission Workflow Version 1
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Run on GalaxyENA Reads & Assembly Submission Workflow
Originally developed within the EVORA project, this two-step Galaxy workflow streamlines submissions to the European Nucleotide Archive (ENA). The workflow first submits raw sequencing reads via the Galaxy ENA upload tool, then submits assembled sequences using the Galaxy ENA Webin CLI tool. The process is fully interactive and GUI-driven while retaining ENA’s required validations leveraging the user-scoped credential management system and the data upload/management from Galaxy.
Step 1 — Raw reads: Galaxy ENA upload tool
A Galaxy wrapper around the ENA-upload-cli that brings a graphical interface and interactive checks to standard ENA read submissions.
Key features
- Raw read submission with ENA-upload-cli at its core
- Use tabular or excel sheet templates to easily capture the metadata
- Client side validation using ENA checklists
- Create, add, and modify ENA objects (e.g., studies, experiments, samples, runs)
Step 2 — Consensus sequences: Galaxy ENA Webin CLI
A Galaxy wrapper around ENA’s Webin-CLI for interactive submission of consensus sequences, with full checklist coverage.
Key features
- Seamless integration with the Galaxy ENA upload tool to fetch and reuse metadata
- Interactive metadata submission and validation
- Support for all assembly levels (contig, scaffold and chromosome)
Funding
The EVORA project has received funding from the European Union's HORIZON programme under grant agreement No 101131959
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Affiliation center | #main/Affiliation center | n/a |
|
| Assembly program | #main/Assembly program | n/a |
|
| Assembly type | #main/Assembly type | n/a |
|
| Chromosome List file | #main/Chromosome List file | n/a |
|
| Consensus sequences | #main/Consensus sequences | n/a |
|
| Coverage | #main/Coverage | The estimated depth of sequencing coverage |
|
| ENA sample checklist | #main/ENA sample checklist | n/a |
|
| Excel file from template | #main/Excel file from template | n/a |
|
| Molecule type | #main/Molecule type | n/a |
|
| Raw reads as dataset lists | #main/Raw reads as dataset lists | n/a |
|
| Submit to ENA test server | #main/Submit to ENA test server | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 11 | ENA Upload tool | toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload/0.9.0+galaxy0 |
| 12 | ENA Webin CLI | ena_webin_cli |
Version History
Version 1 (earliest) Created 24th Oct 2025 at 14:32 by Bert Droesbeke
Initial commit
Frozen
Version-1433b316
Creators and Submitter
Views: 78 Downloads: 5 Runs: 2
Created: 24th Oct 2025 at 14:31
Last updated: 24th Oct 2025 at 14:51
AttributionsNone
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https://orcid.org/0000-0003-0522-5674
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