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nf-core/atacseq: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[1.2.2] - 2022-05-12

  • Minor patch release to fix Conda environment and enable DSL1 by default in the nextflow.config.

Dependencies

  • Update r-base 3.6.2 -> 3.6.3
  • Update r-xfun 0.15 -> 0.22

[1.2.1] - 2020-07-29

  • #118 - Minor patch release to update pipeline schema

[1.2.0] - 2020-07-02

Added

  • #63 - Added multicore support for Trim Galore!
  • #75 - Include gene annotation versions in multiqc report
  • #76 - featureCounts coupled to DESeq2
  • #79 - Parallelize DESeq2
  • #80 - Added social preview image
  • #97 - PBC1, PBC2 from pipeline?
  • #107 - Add options to change MACS2 parameters
  • nf-core/chipseq#153 - Add plotHeatmap
  • nf-core/chipseq#159 - expose bwa mem -T parameter
  • Regenerated screenshots and added collapsible sections for output files in docs/output.md
  • Update template to tools 1.9
  • Replace set with tuple and file() with path() in all processes
  • Capitalise process names
  • Parameters:
    • --bwa_min_score to set minimum alignment score for BWA MEM
    • --macs_fdr to provide FDR threshold for MACS2 peak calling
    • --macs_pvalue to provide p-value threshold for MACS2 peak calling
    • --skip_peak_qc to skip MACS2 peak QC plot generation
    • --skip_peak_annotation to skip annotation of MACS2 and consensus peaks with HOMER
    • --skip_consensus_peaks to skip consensus peak generation
    • --deseq2_vst to use variance stabilizing transformation (VST) instead of regularized log transformation (rlog) with DESeq2
    • --publish_dir_mode to customise method of publishing results to output directory nf-core/tools#585

Fixed

  • #71 - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
  • #73 - macs_annotatePeaks.mLb.clN.summary.txt file is not created
  • #86 - bug in the plot_homer_annotatepeaks.r script
  • #102 - Incorrect Group ID assigned by featurecounts_deseq2.r
  • #110 - updated AWS test GitHub actions
  • #109 - Specify custom gtf but gene bed is not generated from that gtf?
  • nf-core/chipseq#118 - Running on with SGE
  • nf-core/chipseq#132 - BigWig Error: sort: cannot create temporary file in '': Read-only file system
  • nf-core/chipseq#154 - computeMatrix.val.mat.gz files not zipped
  • Make executables in bin/ compatible with Python 3

Dependencies

  • Add bioconductor-biocparallel 1.20.0
  • Add markdown 3.2.2
  • Add pigz 2.3.4
  • Add pygments 2.6.1
  • Add pymdown-extensions 7.1
  • Add python 3.7.6
  • Add r-reshape2 1.4.4
  • Add r-tidyr 1.1.0
  • Update ataqv 1.0.0 -> 1.1.1
  • Update bedtools 2.27.1 -> 2.29.2
  • Update bioconductor-deseq2 1.20.0 -> 1.26.0
  • Update bioconductor-vsn 3.46.0 -> 3.54.0
  • Update deeptools 3.2.1 -> 3.4.3
  • Update fastqc 0.11.8 -> 0.11.9
  • Update gawk 4.2.1 -> 5.1.0
  • Update homer 4.9.1 -> 4.11
  • Update macs2 2.1.2 -> 2.2.7.1
  • Update multiqc 1.7 -> 1.8
  • Update picard 2.19.0 -> 2.23.1
  • Update pysam 0.15.2 -> 0.15.3
  • Update r-base 3.4.1 -> 3.6.2
  • Update r-ggplot2 3.1.0 -> 3.3.2
  • Update r-lattice 0.20_35 -> 0.20_41
  • Update r-optparse 1.6.0 -> 1.6.6
  • Update r-pheatmap 1.0.10 -> 1.0.12
  • Update r-scales 1.0.0 -> 1.1.1
  • Update r-upsetr 1.3.3 -> 1.4.0
  • Update r-xfun 0.3 -> 0.15
  • Update samtools 1.9 -> 1.10
  • Update subread 1.6.4 -> 2.0.1
  • Update trim-galore 0.5.0 -> 0.6.5
  • Update ucsc-bedgraphtobigwig 377 -> 357

[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

[1.0.0] - 2019-04-09

Added

Initial release of nf-core/atacseq Created with version 1.1 of the nf-core template.