Launch on file upload

examples/02 - Launch on file upload.json

This flow uses the Poll files node to periodically check for the presence of a file called RTAcomplete.txt within a Seqera Data Link (eg. an s3 bucket).

These files are typically uploaded by illumina sequencers when base calling is complete. But you could configure it to look for the upload of any file path.

When the file is detected, a List files node is used to list all of the files within that Data Link (bucket - could be configured to use the location that the RTAcomplete.txt file is found).

A Node-RED Function node with some javascript then constructs a sample sheet from these filenames. This is passed to the "Add Dataset" node, which saves it as a Seqera Platform Dataset.

Finally, this is passed to the Launch workflow node, which fires off a pipeline run.

Setup

Some configuration is needed to make this flow work:

• All Seqera nodes need a Seqera configuration to be assigned
• Poll files and List files need to be configured with the name of a Data Link within Platform
• Add dataset needs a dataset name to be set somehow (dynamically to avoid name clashes)
• Launch workflow needs configuring with the name of a Launchpad pipeline, and parameters.