[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