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nf-core/chipseq: Changelog

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

[1.2.1] - 2020-07-29

  • #171 - Minor patch release to update pipeline schema

[1.2.0] - 2020-07-02

Added

  • #138 - Add social preview image
  • #153 - Add plotHeatmap
  • #159 - expose bwa mem -T parameter
  • nf-core/atacseq#63 - Added multicore support for Trim Galore!
  • nf-core/atacseq#75 - Include gene annotation versions in multiqc report
  • nf-core/atacseq#76 - featureCounts coupled to DESeq2
  • nf-core/atacseq#79 - Parallelize DESeq2
  • nf-core/atacseq#97 - PBC1, PBC2 from pipeline?
  • nf-core/atacseq#107 - Add options to change MACS2 parameters
  • 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

Removed

  • --tss_bed parameter

Fixed

  • #118 - Running on with SGE
  • #132 - BigWig Error: sort: cannot create temporary file in '': Read-only file system
  • #154 - computeMatrix.val.mat.gz files not zipped
  • nf-core/atacseq#71 - consensus_peaks.mLb.clN.boolean.intersect.plot.pdf not generated
  • nf-core/atacseq#73 - macs_annotatePeaks.mLb.clN.summary.txt file is not created
  • nf-core/atacseq#86 - bug in the plot_homer_annotatepeaks.r script
  • nf-core/atacseq#102 - Incorrect Group ID assigned by featurecounts_deseq2.r
  • nf-core/atacseq#109 - Specify custom gtf but gene bed is not generated from that gtf?
  • 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 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 phantompeakqualtools 1.2 -> 1.2.2
  • 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

  • nf-core/atacseq#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)
  • nf-core/atacseq#44 - Output directory missing: macs2/consensus/deseq2
  • nf-core/atacseq#45 - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
  • nf-core/atacseq#46 - Stage blacklist file in channel properly
  • nf-core/atacseq#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

[1.0.0] - 2019-06-06

Initial release of nf-core/chipseq pipeline.

Added

  • Raw read QC (FastQC)
  • Adapter trimming (Trim Galore!)
  • Map and filter reads (BWA, picard, SAMtools, BEDTools, BAMTools, Pysam)
  • Create library-size normalised bigWig tracks (BEDTools, bedGraphToBigWig)
  • Alignment QC metrics (Preseq, picard)
  • ChIP-seq QC metrics (deepTools, phantompeakqualtools)
  • Call and annotate broad/narrow peaks (MACS2, HOMER)
  • Create consensus set of peaks per antibody (BEDTools)
  • Quantification and differential binding analysis (featureCounts, DESeq2)
  • Collate appropriate files for genome browser visualisation (IGV)
  • Collate and present various QC metrics (MultiQC, R)