Harshil Patel

We are already removing duplicates with Picard MarkDuplicates right? If so, I would be tempted to use that to remove duplicates before running any downstream peak callers for consistency. This...

Sounds sensible 👍🏽 If we use a single tool like Picard Markduplicates to remove the duplicates then it will be easier to benchmark and compare results downstream.

We would need to think about how we define "replicates" here to use that right? Now that we have removed the `replicate` column from the samplesheet. Maybe we can have...

I did think about having a separate metadata file but why?! Keep it simple and have one would be my preference.

After fishing around the interwebnet it appears that the `dustmasker` executable is now a part of the `BLAST+` suite of tools: https://github.com/tseemann/prokka/issues/256 Creating an `environment.yml` with the contents below provides...

I suspect a `k-mer` based approach is like to be the most efficient way of screening for contaminants in a way where you can pass a relatively unbiased and large...

Hi @Shicheng-Guo ! At this point, we don't have any plans to add WGCNA to the workflow. We have agreed to keep this pipeline to a point where it stops...

Hi @RaverJay ! Did you manage to figure out why this was happening? I haven't seen this issue before and will need a way to reproduce this issue locally in-order...

Hi @JSchoenbachler ! Hope you are well and apologies for the delay. I have tried to reproduce the error you reported but haven't had much luck. Be great if you...

Thanks for giving it a go @JSchoenbachler. I tried to replicate the command you used with a test dataset but if you are still getting the error then I will...