Run Nextflow starting at a certain process

[Daniel H]

Hello, 

Is there a parameter to start at a specific process, and not just the last one that was edited like (it looks like) '-resume' does? 

We are trying to start using a workflow language and are looking at Nextflow. We are wondering if it's possible to start a Nextflow pipeline at a certain process. For instance, if we are building a pipeline with processes a->b->c->d, we would start building and editing a Nextflow file at process a, then start on b, etc. all in the same file. Once earlier steps in the pipeline are working, then we would like to skip earlier processes and just run the one we are currently working on.

I looked through the documentation and saw a '-resume' flag, but it looks like it will resume a pipeline at the earliest modified process since the last running. However, there may be times when edits are made to an earlier process, but we would still like to start at a later one eg. if an earlier process is computationally intense and we only changed a file path or something so it should still be working, and we don't want to run earlier processes despite having made edits to them.

I searched here, on Google, and through the documentation for about an hour but couldn't find anything besides '-resume', so I thought to make a post here.

Thanks, Daniel

[Paolo Di Tommaso]

Hi, 

No, at this time it's not possibile. NF automatically resume from the first modified script to guarantee the consistence of the results. 

My suggestion is to create a mock dataset to iterate quickly in your tests and developments steps. It would allows you to test your pipeline with a CI server such as Travis or Circle. 

Hope it helps. 

Cheers,

Paolo

 

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