How to Submit

1. File preparation

You should have one or more VCF files to submit, as well as a completed metadata spreadsheet following our template. More guidance on these files can be found in the inputs overview as well as in the metadata template itself.

You will also need the reference sequences in FASTA format that you used to generate the VCF files. This is required for validation, though it will not be submitted.

2. Setting up

First install eva-sub-cli, or check that you have the latest version installed.

You will need an ENA Webin account in order to submit, though you can run validation without one.

Finally, you need to specify a submission directory, which is a specific directory associated with each submission. This is where all processing will take place, and where configuration and reports will be saved.

Crucially, the eva-sub-cli tool requires that there be only one submission per directory and that the submission directory not be reused. Running multiple submissions from a single directory can result in data loss during validation and submission.

3. Running eva-sub-cli

The basic command to run validation and submission is as follows:

eva-sub-cli.py --metadata_xlsx <metadata file> --submission_dir <submission directory> --username <webin username> --password <webin password>

This will run validation and generate a report with the results. The report can be viewed as HTML or plain text. More description of the validation checks being performed can be found in the validation overview.

NOTE: If the validation is successful, this command will automatically submit your data and metadata to EVA. If you don’t want this, see below.

If your files are large, we also encourage you to use shallow validation before running full validation and submission.

4. Post submission

Once you’ve successfully validated and submitted your data, you will receive an automatic email stating that your data has been uploaded. If you don’t get this email within a short time, we have very likely not received your data, so you should get in touch with our helpdesk.

If your submission contains human genotype data, then you will also need to provide a signed copy of our consent statement via email. For more information please see our submission FAQs.

Other options

The above steps are the most common, but there are some other options that you can use to tailor its functionality to your needs. A full listing is available by running eva-sub-cli.py -h.

Running only validation or only submission

If you want to run validation without submitting automatically once the validation passes, you can use the --tasks option. To run only validation:

eva-sub-cli.py --metadata_xlsx <metadata file> --submission_dir <submission directory> --tasks VALIDATE

To run only submission - note this will not submit if you’ve not yet validated successfully:

eva-sub-cli.py --metadata_xlsx <metadata file> --submission_dir <submission directory> --tasks SUBMIT --username <webin username> --password <webin password>

Shallow validation

If you are working with large VCF files and find that validation takes a very long time, you can add the argument --shallow to the command, which will validate only the first 10,000 lines in each VCF. Note that running shallow validation will not be sufficient for actual submission but will allow you to identify most validation concerns without long run time.

VCF files and reference FASTA

These can be provided either in the metadata file directly, or on the command line using the --vcf_files and --reference_fasta options. Note that if you are using more than one reference FASTA, you cannot use the command line options; you must specify which VCF files use which FASTA files in the metadata.

VCF files can be either uncompressed or compressed using bgzip. Other types of compression are not allowed and will result in errors during validation. FASTA files must be uncompressed.

Metadata JSON

Frequent submitters may be interested in using our metadata JSON schema instead of our spreadsheet template. The metadata requirements are the same regardless of which format you use, you will just need to use the --metadata_json option instead of the --metadata_xlsx option.

Running using Docker

If you’ve installed eva-sub-cli using Docker, make sure that Docker is running in the background before running eva-sub-cli, e.g. by opening Docker Desktop. Additionally, for each eva-sub-cli command, add the command line option --executor docker, which will fetch and manage the Docker container for you.

Using Nextflow

Under the hood, eva-sub-cli uses Nextflow to run validation, which you can configure on the command line using the --nextflow_config option. For more information, please see here.