Workflow plugins provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).

https://github.com/DKFZ-ODCF/IndelCallingWorkflow

https://github.com/DKFZ-ODCF/RNAseqWorkflow

https://github.com/DKFZ-ODCF/ACEseqWorkflow

https://github.com/DKFZ-ODCF/SNVCallingWorkflow

https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows

OR

https://github.com/ghga-de/nf-aceseq

https://github.com/ghga-de/nf-platypusindelcalling

https://github.com/ghga-de/nf-snvcalling