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Submission automation

These scripts are meant to be used by EVA helpdesk personnel to manage submissions to the EVA. They process the submission in a semi-automated way and record the outcome of each step in a yaml file located in a given submission directory

Scripts

Information about a submission

The following script simply surveys the content of FTP boxes and returns a short text that should provide enough information to create the submission ticket.

python detect_submission.py --ftp_box 3 --submitter john

Copy relevant file to the submission folder

This script can be used to grab the relevant files from the ftp_box and to copy them to the submission folder when you supply --ftp_box and --submitter parameters. It will also prepare the submission folder and create the directory structure and the config file required for the rest of the execution. Without the above parameters, it only prepares the submission folder.

python prepare_submission.py --ftp_box 3 --submitter john --eload 677

or

python prepare_submission.py --eload 677

Validate the submitted data

This script will run the validation required to ensure that the data is suitable to be archived. It will check

  • The metadata spreadsheet format (metadata_check)
  • The sample names in the VCF and metadata matches (sample_check)
  • The VCF conforms to the submission standards (vcf_check)
  • The VCF reference allele match the reference genome. (assembly_check)

At the end of the run if all the validation pass the script will register the input vcf and metadata as valid in the config file.

python validate_submission.py --eload 677

This command will output a report to standard output to detail the validation results.

You can run only part of the validation by specifying the validation task

python validate_submission.py --eload 677 --validation_tasks metadata_check

The valid values for the validation tasks are: metadata_check, sample_check, vcf_check, and assembly_check

You can also force a validation to pass by specifying the flag --set_as_valid. This will mark all validation tasks performed as Forced.

Brokering to BioSamples and ENA

Once the validation pass and VCF files and metadata are marked as valid, the brokering can start. It will:

  • Index the VCF file(s) and calculate their md5
  • Create BioSamples entries in BioSamples
  • Upload the VCF files to ENA
  • Create and upload ENA XML files
  • Parse and store the submission, project and analysis accession
python broker_submission.py --eload 677

You can specify a list of VCF and/or a metadata file on the command line to override the one set in the config file by the validation step.

python broker_submission.py --eload 677 --vcf_files /path/to/vcf1.vcf /path/to/vcf2.vcf --metadata_file /path/to/metadata.xlsx

You can specify a project accession to add the analysis to this ENA project. The project must exist and be writable.

python broker_submission.py --eload 677 --project_accession PRJEB00001

Data ingestion

After validation and brokering are done, the data can be loaded into our databases and made publicly available. This involves four main steps:

  1. Loading submission metadata from ENA into EVAPRO (metadata_load)
  2. Accessioning VCF files and making files public (accession)
  3. Loading into the variant warehouse (variant_load)
  4. Clustering in the current supported assembly, including remapping to that assembly if necessary (optional_remap_and_cluster)

By default, the script will run all of these tasks, though you may specify a subset using the flag --tasks. Note that as some steps are long-running the script is best run in a screen/tmux session.

# To run everything 
python ingest_submission.py --eload 765

# Only variant load 
python ingest_submission.py --eload 765 --tasks variant_load

# Only run VEP annotation - note this assumes variant load has been run
python ingest_submission.py --eload 765 --tasks annotation

Backlog automation

Older studies that have been manually brokered will need to have a preparation script run before ingestion automation. This will create the config file and run validation on the VCF files (without metadata validation) to ensure they are up to current standards.

python prepare_backlog_study.py --eload 506

If the config file already exist, the prepare_backlog script will not do anything, you can override this by specifying the --force_config option

python prepare_backlog_study.py --eload 506

You can also specify only a subset of the validation tasks to perform

python prepare_backlog_study.py --eload 506  --validation_tasks aggregation_check

If the files are valid then ingestion can be run as usual.

Config upgrade

There is also a script to upgrade an existing config file for a submission so that it is compatible with the current version of the submission automation scripts. This is automatically invoked when necessary, but it can also be run on its own, e.g. when an analysis alias can't be determined automatically.

python upgrade_config.py --eload 506 --analysis_alias alias

Submission migration

To migrate a submission from Noah to Codon at any stage in processing, the following script will copy directories and update paths in the config.

# Run in Codon
python migrate_submission.py --eload 506

# If there's also a project directory to copy
python migrate_submission.py --eload 506 --project PRJEB12345