I'm not entirely sure that the current workflow can be included as a subworkflow for other Nextflow workflows. Can you demonstrate this functionality?

[Juke34]

No description provided.

[Juke34]

I have added a section "Integrating AliNe in another nf pipeline" in the README and added a citation in the paper pointing to the proof of concept on how to integrate a workflow in another workflow.

@rcannood Is it enough to answer your concern?

[rcannood]

I appreciate the edits that you made. However, in terms of functionality, I'm not able to confirm that AliNe offers the functionality that is claimed in the paper. As such, I'd be inclined to change the text such that users are informed that ways of daisy chaining nextflow workflows exist and that this could be explored to further improve the usability of AliNe. What do you think?

[Juke34]

I understand your concern. Here what I have done :

I've created a repository to illustrate how to do a daisy chaining with Aline here and refer to it in the text.

I also updated the paragraph as follow:

Furthermore, leveraging the concept of daisy-chaining Nextflow workflows [@nfcascade], AliNe can be integrated as a sub-workflow within other Nextflow pipelines [@daisychainingaline], providing a standardized alignment step while offering a diverse selection of alignment tools.

Is this enough to answer your comment?