Added

• 1494fff - Update pipeline template to nf-core/tools 2.12
• ec24cfb - Update pipeline template to nf-core/tools 2.11.1
• 15b8ff3 - Update pipeline template to nf-core/tools 2.11
• 9712163 - Update pipeline template to nf-core/tools 2.10
• #130 - AWS Mega Tests
• #132 - Add Bowtie 2 as an aligner option

Changed

• #117 - Use fromSamplesheet
• Updating naming scheme to use things from the Dune universe

Fixed

• [#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

Added

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

Changed

• [#103] - Updated Modules

Fixed

• [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)

Added

• 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

Fixed

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

Dependencies

• 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.