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Published November 5, 2019 | Version 1.1.0
Software Open

nf-core/atacseq: nf-core/atacseq v1.1.0 - Iron Shark

Authors/Creators

  • 1. The Francis Crick Institute
  • 2. Science for Life Laboratory
  • 3. @qbicsoftware

Description

[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

Files

nf-core/atacseq-1.1.0.zip

Files (1.5 MB)

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Additional details

Related works

Is supplement to
https://github.com/nf-core/atacseq/tree/1.1.0 (URL)