nf-core/atacseq v1.1.0 - Iron Shark

[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