Version history


  • [#109] - Fixed bug where using AWS igenomes or passing a pre-made index fails because of an update to the module expects them to have a metamap. Generation was still working. (@MathewBerg9)

Full Changelog:…2.1.1


  • [#94] - Added a second BEDTools intersect step to allow filtering and overlapping in the same workflow. (@Emiller88)
  • [#101] - Initialized nf-test (@Emiller88 )


  • [#103] - Updated Modules



  • DSL2 conversion
  • [#28] - Added DRAGMAP alignment
  • [#64] - Added CHM13 igenomes config
  • [#39] - Add PINTS for TSS identification
  • [#71] - Add FASTP for adapter trimming
  • [#77] - Add dedup subworkflow


  • [#33] - groHMM works on full runs. Added the keep standard chromosomes function to standardize bam files.


  • Updated Nextflow version to v21.10.6

Initial release of the nf-core/nascent transcription processing pipeline made by @ignaciot @magruca !

This pipeline is designed to process the sequencing output of nascent transcription assays, like GRO-seq or PRO-seq. It produces bedGraph- and bigWig-formatted outputs after mapping strand-specific reads, as well as other useful outputs like quality control reports or IGV-ready (Integrative Genomics Viewer) TDF files.