- [#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: https://github.com/nf-core/nascent/compare/2.1.0…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
- [841ae62] - Updated PINTS version from 1.1.6 to 1.1.8 (Fixes an issue where PINTS fails if one of the predictions was empty) (@Emiller88)
- [#97] - Add HOMER channels to fix error about “Missing workflow output parameter: homer_peaks” when homer is skipped (@Emiller88
- Add missing DOIs (@apeltzer)
- 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
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.