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.
- #46 - Missing gene_bed path in igenomes config
- Update template to tools
1.7 - Add
--trim_nextseqparameter - Add
CITATIONS.mdfile - Capitalised process names
- Change all parameters from
camelCasetosnake_case(see Deprecated) - #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
- Increase default resource requirements in
base.config - Increase process-specific requirements based on user-reported failures
- Update Nextflow
0.32.0->19.10.0
| Deprecated | Replacement |
|---|---|
--design |
--input |
--singleEnd |
--single_end |
--saveGenomeIndex |
--save_reference |
--skipTrimming |
--skip_trimming |
--saveTrimmed |
--save_trimmed |
--keepDups |
--keep_dups |
--keepMultiMap |
--keep_multi_map |
--saveAlignedIntermediates |
--save_align_intermeds |
--narrowPeak |
--narrow_peak |
--saveMACSPileup |
--save_macs_pileup |
--skipDiffAnalysis |
--skip_diff_analysis |
--skipFastQC |
--skip_fastqc |
--skipPicardMetrics |
--skip_picard_metrics |
--skipPreseq |
--skip_preseq |
--skipPlotProfile |
--skip_plot_profile |
--skipPlotFingerprint |
--skip_plot_fingerprint |
--skipSpp |
--skip_spp |
--skipIGV |
--skip_igv |
--skipMultiQC |
--skip_multiqc |
Initial release of nf-core/chipseq pipeline.
- Raw read QC (FastQC)
- Adapter trimming (Trim Galore!)
- Map and filter reads (BWA, picard, SAMtools, BEDTools, BAMTools, Pysam)
- Create library-size normalised bigWig tracks (BEDTools, bedGraphToBigWig)
- Alignment QC metrics (Preseq, picard)
- ChIP-seq QC metrics (deepTools, phantompeakqualtools)
- Call and annotate broad/narrow peaks (MACS2, HOMER)
- Create consensus set of peaks per antibody (BEDTools)
- Quantification and differential binding analysis (featureCounts, DESeq2)
- Collate appropriate files for genome browser visualisation (IGV)
- Collate and present various QC metrics (MultiQC, R)