nf-core/nascent
Nascent Transcription Processing Pipeline
gro-seqnascentpro-seqrnatranscriptiontss
Version history
What’s Changed
- Use singularity containers for PINTS by @edmundmiller in https://github.com/nf-core/nascent/pull/137
- Pass references as inputs by @edmundmiller in https://github.com/nf-core/nascent/pull/139
- Add HISAT2 by @edmundmiller in https://github.com/nf-core/nascent/pull/140
- build: Fix modules.json and bump subworkflows by @edmundmiller in https://github.com/nf-core/nascent/pull/141
- Add STAR aligner by @edmundmiller in https://github.com/nf-core/nascent/pull/142
- Update Modules by @edmundmiller in https://github.com/nf-core/nascent/pull/147
- Add citations to MultiQC by @edmundmiller in https://github.com/nf-core/nascent/pull/149
- Fix HOMER inputs by @edmundmiller in https://github.com/nf-core/nascent/pull/151
- Refactor tests by @edmundmiller in https://github.com/nf-core/nascent/pull/152
- Update HOMER docs by @edmundmiller in https://github.com/nf-core/nascent/pull/154
- Use BAM_RSEQC subworkflow by @edmundmiller in https://github.com/nf-core/nascent/pull/155
- Use official nf-test CI by @edmundmiller in https://github.com/nf-core/nascent/pull/157
- Cleanup output by @edmundmiller in https://github.com/nf-core/nascent/pull/156
- Fix GFFREAD bug by @edmundmiller in https://github.com/nf-core/nascent/pull/162
- style: Make version snapshots pretty by @edmundmiller in https://github.com/nf-core/nascent/pull/163
- Dynamic BWA MEM index memory by @edmundmiller in https://github.com/nf-core/nascent/pull/166
- Fix “Access to undefined parameter
forwardStranded
” warnings by @edmundmiller in https://github.com/nf-core/nascent/pull/170 - Clean up MultiQC and tests by @edmundmiller in https://github.com/nf-core/nascent/pull/171
- groHMM overhaul by @edmundmiller in https://github.com/nf-core/nascent/pull/165
- PINTS scatter gather by @edmundmiller in https://github.com/nf-core/nascent/pull/174
- Add HOMER uniqmap by @edmundmiller in https://github.com/nf-core/nascent/pull/175
- Clean groHMM publishing and remove
each
inputs by @edmundmiller in https://github.com/nf-core/nascent/pull/178 - chore: Remove old template by @edmundmiller in https://github.com/nf-core/nascent/pull/179
- Adopt nft-utils by @edmundmiller in https://github.com/nf-core/nascent/pull/182
- test(#57): Add uniqmap test by @edmundmiller in https://github.com/nf-core/nascent/pull/177
- chore: Fix config selectors by @edmundmiller in https://github.com/nf-core/nascent/pull/173
- Run lsp formatting by @edmundmiller in https://github.com/nf-core/nascent/pull/180
Full Changelog: https://github.com/nf-core/nascent/compare/2.2.0…2.3.0
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.