All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- #35 - Add deepTools plotFingerprint
- #46 - Missing gene_bed path in igenomes config
- Merged in TEMPLATE branch for automated syncing
- Update template to tools
1.7 - Add
CITATIONS.mdfile - Capitalised process names
- Add parameters:
--seq_center--trim_nextseq--fingerprint_bins--broad_cutoff--min_reps_consensus--save_macs_pileup--skip_diff_analysis--skip_*for skipping QC steps
- Change all parameters from
camelCasetosnake_case(see Deprecated) - #41 - Docs: Add example plot images
- #44 - Output directory missing: macs2/consensus/deseq2
- #45 - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
- #46 - Stage blacklist file in channel properly
- #50 - HOMER number of peaks does not correspond to found MACS2 peaks
- Fixed bug in UpSetR peak intersection plot
- IGV now uses relative instead of absolute paths
- Smaller logo for completion email
- Renamed all channels to start with
ch_prefix - Increase default resource requirements in
base.config - Increase process-specific requirements based on user-reported failures
- Update Nextflow
0.32.0->19.10.0 - Add preseq
2.0.3 - Add deeptools
3.2.1 - Add r-xfun
0.3 - Add gawk
4.2.1
| Deprecated | Replacement |
|---|---|
--design |
--input |
--singleEnd |
--single_end |
--saveGenomeIndex |
--save_reference |
--skipTrimming |
--skip_trimming |
--saveTrimmed |
--save_trimmed |
--keepMito |
--keep_mito |
--keepDups |
--keep_dups |
--keepMultiMap |
--keep_multi_map |
--skipMergeReplicates |
--skip_merge_replicates |
--saveAlignedIntermediates |
--save_align_intermeds |
--narrowPeak |
--narrow_peak |
Initial release of nf-core/atacseq Created with version 1.1 of the nf-core template.