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                                            Kevin Menden

Refgenie Integration (Overview)

## Refgenie Integration Overview Issue This issue is to track the different tasks/issues/PRs related to the integration of Refgenie to nf-core. ### Build local Nextflow config with Refgenie paths -...

template

command line tools

Adapt `nf-core licences` for DSL2

The command `nf-core licences` currently only works for DSL1 pipelines as it uses the `environment.yml` file to fetch the licences of all bioconda tools. This file is missing from DSL2...

DSL2

Scaden example sometimes breaks

bug

Enable multiprocessing for data simulation

Data simulation can be done with multiple threads/processes relatively easily.

enhancement

Automatic cell type labeling for easier data preparation

Currently the biggest hurdle for using Scaden is to prepare the training data. This could be substantially eased by developing a semi-automatic pipeline (or maybe fully automatic), which converts raw...