Zlatko Mašek - Nov 03, 2022

Importing samples from existing projects

tl;dr: samples already on the Gencove platform can now be easily reprocessed using a different project configuration.

Previously, FASTQ files could only be imported using the Gencove CLI, or Amazon S3 and Illumina BaseSpace integrations. The Gencove platform can now use FASTQ files of one analyzed sample directly as a source for another sample in a different project. Provided that everything is in order (e.g. user permissions, availability of files), importing existing samples is straightforward. This speeds up the process where it's necessary to analyze the same sample with different project configurations.

Importing samples to a different project can be done using the Gencove web interface or the Gencove CLI.

Importing samples from existing projects using the Gencove web interface

Select the samples in the list then click on the button “Send to project” in the top right corner:

Select the project where you want to send the samples and click “Send to project”:

Press “Run analysis” button to immediately start processing the sent samples:

The destination project will have the new samples set in the “running” status when this is done.

Importing samples from existing projects using the Gencove CLI

This can also be done through the CLI itself:

$ gencove projects import-existing-samples \
 <destination-project-id> \
 --sample-ids <source-sample-id-1>,<source-sample-id-2> \
 --metadata-json='{"batch": "batch1"}'

More information on how to import the existing samples is available in the Gencove documentation and, as always, let us know what you think.