[1.1.0] - 2019-11-05 Added #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.md file 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 Fixed Change all parameters from camelCase to snake_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 Dependencies 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 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