nf-core/chipseq: 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