Skip to content

CHANGELOG.md

Latest commit

 

History

History
137 lines (106 loc) · 5.41 KB

CHANGELOG.md

File metadata and controls

137 lines (106 loc) · 5.41 KB

Changelog

All notable changes to this project will be documented in this file.

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

0.0.4

Added

  • Add ability to downsample total reads to match in group normalization
  • Add conversion from bigwig to bedgraph and wig formats
  • Ability to calculate queries at lower resolutions with bwtools
  • Ability to downsample aligned data based on group minimum
  • Gini coefficient calculations for NETseq data
  • Pseudoalignment with Kallisto for stranded data
  • Modeling with Sleuth
  • Seperation of feature counting from modeling
  • Stranded querys with sense and antisense capabilities bwtools_query_stranded
  • Stranded spike-in normalization using variety of methods including Bonhoure et al. method and DEseq2 method
  • Deduplication with Picard MarkDuplicates.
  • Ability to set specific locations to zero when doing NETseq pause calling
  • Give background corrected logos in NETseq
  • Specify whether you want sequences pulled for NET-seq pauses or not
  • Ability to plot large logos for NET-seq
  • More pause calling types for NET-seq
  • Ability to skip mark duplicates for bams

Changes

  • Update versions of some packages including ncbi-acc-download to get around rate filtering issue and multiqc to deal with python updates
  • Enable the ability to choose which QC you want to run
  • Allow fasta files to complement full IUPAC nomenclature i.e. R complements Y.

Bug fixes

  • Issue with syntax of comparisons in coverage_and_norm.smk
  • Issue with using not input_sample.isnull() in higher version of snakemake
  • Issue with bwtools_multiprocessing not correctly identifying needed input files
  • Fixed issues with sample sheets that do not have a input_sample or only have single end samples
  • Fixed bug in NETseq pause calling that would only report last chromosome

0.0.3

Added

  • Added a log2 strand bias calculation as a possible coverage track
  • Calculation of the count of fragments for each contig
  • Allow two separate cutadapt runs to occur for sequencing kits that require sequential trimming
  • Added a rule to generate annotation files easily with run_annotations
  • Added the ability to specify relative coordinates in bwtools_query
  • Unstranded Peak calling and motif calling
  • Modeling module with DESeq2 and stranded feature quant with HTseq-count
  • Ability to better set parameters for ChIP QC in config file

Changed

  • Refactored NETseq_pause_calling.py for performance boost

Bug fixes

  • Fixed issue with workflow/rules/coverage_and_norm.smk extending reads for non-paired end samples
  • Fixed issue with multiqc report not properly reporting pre and post trim fastqc reports
  • Fixed issue with bamPEFragmentSize would attempt to run on single end data
  • Fixed issue with trimmomatic not properly running for single end data
  • Fixed issue with spearman correlation calculations failing on updated coverage files from bwtools
  • Fixed issue with NETseq pause calling failing when NaNs were present in data by coercing all NaNs to zeros
  • Fixed issue where pulling sequences from bed files near genome boundaries would fail. Updated to consider all chromosomes as circular.
  • Fixed an issue where NETseq logos would display information content on a non-standard scale. Fixed scaling to be 0 to 2.0 bits
  • Fixed an issue where numpy deprecations impact deeptools quality control. Set a lower version of numpy in environment files for quality control

0.0.2

Added

  • Add ability to get combined annotation table and bed for genome annotations

Bug fixes

  • Fixed bug preventing stranded coverage under some normalization schemes

0.0.1

  • Added ability to process coverage in a stranded manner
  • Added support for NET-seq data
  • Added limited support for bisulfite data

ChIPseq pipeline change log before fork

0.2.8 - 2021-01-20

Added

  • Ability to collapse multiple bigwig files into one using summary stats
  • Ability to perform operations between two groups of bigwig files

0.2.7 - 2021-01-10

Added

  • Added support for single end libraries

0.2.6 - 2021-12-08

Added

  • Added relative polymerase progression calculation to bwtools_query (http://dx.doi.org/10.1016/j.molcel.2014.02.005)
  • Add the ability to smooth raw signals using convolution with a Gaussian or flat kernel.
  • Add the ability to smooth raw signals using a Savitzky-Golay filter
  • Ability to calculate the region-level spearman correlations for a set of samples in bwtools_query
  • Add calculations of the traveling ratio (10.1016/j.molcel.2008.12.021)
  • Add discovery of a local max within a region

Changed

  • Output of bwtools_query is now compressed (gzip). File extension changed to .tsv.gz

0.2.5 - 2021-10-25

Added

  • Allow mix and match between querysub, queryscale fixedsub, and fixedscale.

0.2.4 - 2021-10-13

Added

  • Create a compiled html table of all mutations called across all samples in variant_calling

Bug fixes

  • Fixed a bug in renaming sample/output/output.gd files to renamed_output/sample.gd in variant_calling

0.2.3 - 2021-10-12

Added

  • A variant_calling module to call changes from the reference genome with ChIP input samples (#2)
  • Add option to control what fraction of a region can have NaNs in it and still report a summary value in bwtools query