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mribeirodantas committed Oct 9, 2024
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Nextflow workflows are widely used across various fields, performing tasks ranging from data retrieval and cleaning to processing and downstream analyses. Generally, workflows which feed into other workflows are run independently. They are also often not written in a way they can be included directly as subworkflows into another workflow, making it challenging to connect them seamlessly. [nf-cascade](https://github.com/mahesh-panchal/nf-cascade) is a proof-of-concept pipeline that demonstrates how multiple existing workflows can be integrated into a single workflow. Specifically, the proof-of-concept connects the nf-core pipelines: nf-core/fetchngs, nf-core/taxprofiler, nf-core/mag, and nf-core/funcscan. The code can be generalised further to run and connect any existing workflow, without any modifications necessary to the workflows you want to run.
Nextflow workflows are widely used across various fields, performing tasks ranging from data retrieval and cleaning to processing and downstream analyses. Generally, workflows which feed into other workflows are run independently. They are also often not written in a way they can be included directly as subworkflows into another workflow, making it challenging to connect them seamlessly. [nf-cascade](https://github.com/mahesh-panchal/nf-cascade) is a proof-of-concept pipeline that demonstrates how multiple existing workflows can be integrated into a single workflow. Specifically, the proof-of-concept connects the nf-core pipelines: [nf-core/fetchngs](https://nf-co.re/fetchngs/), [nf-core/taxprofiler](https://nf-co.re/taxprofiler/), [nf-core/mag](https://nf-co.re/mag/), and [nf-core/funcscan](https://nf-co.re/funcscan/). The code can be generalised further to run and connect any existing workflow, without any modifications necessary to the workflows you want to run.

The inspiration for nf-cascade came from a question on the Nextflow Slack workspace. A member of the community wanted to benchmark a set of tools and compare them with their own workflow. They needed a way to run their Nextflow workflow within another Nextflow workflow while still utilising container technologies and cluster submission systems.
The inspiration for nf-cascade came from a question on the [Nextflow Slack workspace](https://www.nextflow.io/slack-invite.html). A member of the community wanted to benchmark a set of tools and compare them with their own workflow. They needed a way to run their Nextflow workflow within another Nextflow workflow while still utilising container technologies and cluster submission systems.

I proposed running Nextflow natively using a process with [exec:](https://www.nextflow.io/docs/latest/process.html#native-execution). Processes that use exec: execute Groovy code natively, meaning they run locally in the same environment as the Nextflow runner. This allows the child Nextflow workflow to access the same environment as the parent workflow, enabling the use of the same tools for both (e.g., the same container platform and same job scheduler).

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