The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- 5bcfe4f - Update pipeline template to nf-core/tools 2.13
- a3bc907 - Update pipeline template to nf-core/tools 2.13.1
- #140 - Add HISAT2 aligner
- #142 - Add STAR aligner
- #149 - Add Software citations to MultiQC
- #175 - Add HOMER uniqmap support
- a3bc907 - Update pipeline template to nf-core/tools 2.13.1
- 14fdbb8 - Update pipeline template to nf-core/tools 3.0.0
- b4ac8c5 - Update pipeline template to nf-core/tools 3.0.1
- a9ae47a - Update pipeline template to nf-core/tools 3.0.1
- bfcd97c - Update pipeline template to nf-core/tools 3.1.0
- 7a4e356 - Update pipeline template to nf-core/tools 3.1.1
- 7a4e356 - Update pipeline template to nf-core/tools 3.1.2
- 7a4e356 - Update pipeline template to nf-core/tools 3.2.0
- 852b5f0 - Update pipeline template to nf-core/tools 3.2.1
- #171 - Clean up MultiQC report
- #170 - Remove "Access to undefined parameter forwardStranded" warnings
- #173 - Fix config selectors
- #173 - Remove STAR transcriptome run
- #137 - Use singularity containers for PINTS
- #142 - Updated CHM13 references
- #171 - Use assertAll in tests
- #165 - groHMM overhaul. Removed R mclapply calls and replaced with Nextflow scatter gather for parameter tuning. This creates a job for each parameter set.
- #174 - PINTS Scatter gather pattern by chromosome
- #178 - Remove groHMM parameter tuning publishing and remove
eachinputs from parameter tuning module
- [#165] - Removed support for groHMM tuning files.
- 9712163 - Update pipeline template to nf-core/tools 2.10
- 15b8ff3 - Update pipeline template to nf-core/tools 2.11
- ec24cfb - Update pipeline template to nf-core/tools 2.11.1
- 1494fff - Update pipeline template to nf-core/tools 2.12
- [#130] - AWS Mega Tests
- [#132] - Add Bowtie 2 as an aligner option
- [#117] - Use fromSamplesheet
- [#109] - 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.
- [#94] - Add a second BEDTools intersect step to allow filtering and overlapping in the same workflow.
- [#101] - Initialized nf-test
- [#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)
- [#97] - Add HOMER channels to fix error about "Missing workflow output parameter: homer_peaks" when homer is skipped
- Add missing DOIs (@apeltzer)
- DSL2 conversion
- [#28] - Add DRAGMAP alignment
- [#64] - Add 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
Update to the container to meet the latest template requirements, and dependencies for new features in an upcoming PR (R and Picard tools).
Initial release of nf-core/nascent, created with the nf-core template.