nf-core/chipseq v1.1.0 - Platinum Pig

[1.1.0] - 2019-11-05

Added

• #46 - Missing gene_bed path in igenomes config
• Update template to tools 1.7
• Add --trim_nextseq parameter
• Add CITATIONS.md file
• Capitalised process names

Fixed

• Change all parameters from camelCase to snake_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

Dependencies

• Update Nextflow 0.32.0 -> 19.10.0

Deprecated

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