Leto

What's Changed

• Use singularity containers for PINTS by @edmundmiller in #137
• Pass references as inputs by @edmundmiller in #139
• Add HISAT2 by @edmundmiller in #140
• build: Fix modules.json and bump subworkflows by @edmundmiller in #141
• Add STAR aligner by @edmundmiller in #142
• Update Modules by @edmundmiller in #147
• Add citations to MultiQC by @edmundmiller in #149
• Fix HOMER inputs by @edmundmiller in #151
• Refactor tests by @edmundmiller in #152
• Update HOMER docs by @edmundmiller in #154
• Use BAM_RSEQC subworkflow by @edmundmiller in #155
• Use official nf-test CI by @edmundmiller in #157
• Cleanup output by @edmundmiller in #156
• Fix GFFREAD bug by @edmundmiller in #162
• style: Make version snapshots pretty by @edmundmiller in #163
• Dynamic BWA MEM index memory by @edmundmiller in #166
• Fix "Access to undefined parameter forwardStranded" warnings by @edmundmiller in #170
• Clean up MultiQC and tests by @edmundmiller in #171
• groHMM overhaul by @edmundmiller in #165
• PINTS scatter gather by @edmundmiller in #174
• Add HOMER uniqmap by @edmundmiller in #175
• Clean groHMM publishing and remove each inputs by @edmundmiller in #178
• chore: Remove old template by @edmundmiller in #179
• Adopt nft-utils by @edmundmiller in #182
• test(#57): Add uniqmap test by @edmundmiller in #177
• chore: Fix config selectors by @edmundmiller in #173
• Run lsp formatting by @edmundmiller in #180

Full Changelog: 2.2.0...2.3.0

Usul

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

Tin Snake

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: 2.1.0...2.1.1

Aluminium Squirrel

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)

Titanium Oyster

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

nf-core/nascent version 1.0

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.