James A. Fellows Yates
James A. Fellows Yates
that's also something I partly considered: the competitive mapping is used for very specific contexts (e.g. strain discrimination during pathogen screening), and like you said sort of breaks some assumptions...
@ggabernet @ssnn-airr is this still needed? Or can we close it?
nf-core module exists already if someone fancies jumping on this ;)
I thought that until I saw: "Note that AuthentiCT only applies to sequences generated from single-stranded libraries and is not tailored for the more complex deamination patterns of sequences generated...
More notes from: https://github.com/nf-core/eager/issues/597#issue-732190581
Note it's now on github and pip, but will need to be added to bioconda @TCLamnidis https://github.com/StephanePeyregne/AuthentiCT
Basically need to ensure if jobs go above the `shared` node configuration, it switches to the _minimum_ requirements for the exclusive nodes. i.e., you go above ``` shared cpu 36...
Also seems to be a `maxFork` limit of 16 jobs on exclusive nodes
Hi @xhejtman, yes sorry about that. Unfortunately this was derived from a (persisting) lack of understanding of how java deals with memory as on my part. This will be fixed...
> A DAG diagram of where reads are ending up as inputs to other tools would be a huge help for interpretability of the pipeline, and as a potential ""dry""...