Chaining Pipelines Together

Open to adding any more solutions.

0 voters

Nextflow in Nextflow means either using a Nextflow process for each workflow (Similar to the Snakemake wrapper) or importing each workflow as a subworkflow of another workflow.


Bash scripts seems to be the simplest option to me, by nextflow in nextflow do you mean using nextflow process for each workflow or import each workflow?

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Using Nextflow within Nextflow would theoretically improve the overall harmony of the process. It would enable the resumption of work across two chained pipelines with -resume, enable combined execution reporting of Nextflow, and automate workflow orchestration more effectively when running on AWS Batch. Additionally, it is likely to simplify the establishment of ‘best practice’ guidelines for pipeline development. While implementing bash might seem straightforward, it could result in a wild west :cowboy_hat_face: with more unstructured and a diverse range of methods for achieving chaining and execution.

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Ah, I missed those. I was interested in the break-down, so let’s call it either of them, since I can’t update the poll.