Hi all, wondering if there's an option to run multiple samples without them being concatenated? Or do we need to run the pipeline multiple times, one per sample, if we want to keep the assemblies separate?

Hi Isaac, currently there is no option to run multiple samples without them being concatenated for creating the assembly. Feel free to open a github issue for this if you feel like it is a feature that would be used often. For now, you would have to run the pipeline multiple times with one sample per run

Thanks for the clarification 🙂

@Avani Bhojwani This is actually the exact issue that I solved in my old pipeline with the '.collectFile' and re-reading in the file hack. It's due to the annoying fact that .collect() waits for inputs but combines different workflow outputs and has no option to prevent this

How do the other pipelines like Sarek handle this? I'm certain that I've been able to run different samples and keep them separate in the past with Sarek

It sounds doable, I just haven't looked into it as I assumed most people would want just one assembly when creating the pipeline. and also due to time constraints currently

@Isaac W I haven't checked that exact pipeline (I certainly should do so), but one factor that may complicate it is combining the output of different assemblers together, but where the user can specify only to use some of the assemblers. So we need an input workflow that waits for all specified workflows to finish. Many other pipelines have pre-defined numbers of inputs for each process, whereas here it is a design feature that the user can vary the assemblers used, at teh expense of there being no obvious way to do multiple different sample assemblies at once.