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Restructuring
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jaymedina committed Jan 12, 2024
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Expand Up @@ -15,8 +15,8 @@ This Python package provides the components to connect various third-party servi

This repository includes a demonstration script called [`demo.py`](demo.py), which showcases how you can use `py-orca` to launch and monitor your workflows on Nextflow Tower. Specifically, it illustrates how to process an RNA-seq dataset using a series of workflow runs, namely `nf-synstage`, `nf-core/rnaseq`, and `nf-synindex`. `py-orca` can be used with any Python-compatible workflow management system to orchestrate each step (_e.g._ Airflow, Prefect, Dagster). The demonstration script uses [Metaflow](https://metaflow.org/) because it's easy to run locally and has an intuitive syntax.

The script assumes that the following environment variables are set. Before setting up these environment variables, ensure that you have an AWS profile configured for a role that has access to the dev/ops tower workspace you plan to launch your workflows from.
Refer to [`.env.example`](.env.example) for the format of their values as well as examples. You can set these environment variables using whatever method you prefer (_e.g._ using an `.env` file, sourcing a shell script).
The script assumes that the following environment variables are set. Before setting them up, ensure that you have an AWS profile configured for a role that has access to the dev/ops tower workspace you plan to launch your workflows from. You can set these environment variables using whatever method you prefer (_e.g._ using an `.env` file, sourcing a shell script).
Refer to [`.env.example`](.env.example) for the format of their values as well as examples.

- `NEXTFLOWTOWER_CONNECTION_URI`
- `SYNAPSE_CONNECTION_URI`
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