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