Christian Mertes

Test if the pipeline works if only external counts are provided

This will close #154

Dear @scharf-f , Thank you for trying out DROP and thank you for the detailed report. I'm still working on the import functionality for splicing counts. Its currently under development....

Exactly. But we also have to make sure that the pipeline is rerun when dependencies change based on the grouping of samples. We could create an input file while checking...

I added this new functionality to add external splicing counts. Currently, we have only a dataset for fibroblasts from the Kremer paper for `hg19`. If you have time and interest...

thanks @HenrikBengtsson this was really helpful. I can confirm that the `RhpcBLASctl::omp_set_num_threads(1L)` did the trick for us and now it is also running through on my WSL. Since we do...

Just wanted to leave my two cents here as we had already some issues with this too (referring to: https://github.com/drisso/zinbwave/issues/38#issuecomment-656256405). As of my knowledge BiocParallel ignores SLURM, Snakemake or other...

Sorry for not being too clear on this @mtmorgan. `Batchtools` is great if you want to parallelize within R across a cluster, but I was referring to the scenario where...

Thank you @FriederikeHanssen for tagging me. Yes, indeed this is a goal of GHGA to automate benchmarking in a kind of CI/CD fashion. We currently do this together with the...

We also use the hap.py + eval on a GIAB sample with some extra tweaks. Currently, the pipeline is written in snakemake.