Change log

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

Unreleased

  • Improve interaction with BiocProject auto-loading results in R.

[0.8.6] -- 2019-03-26

Changed

  • Use ngtsk ziptool option universally
  • Change how tools are parameterized and include bowtie2
  • Simply and clarify prealignment steps
  • Improve argument order for better readability

Added

  • Perform a pre-check that all required tools are callable
  • Add multiple targets and a pre-check for FIFO usage

[0.8.5] -- 2019-03-19

Changed

  • Convert and update documentation
  • Fixed a bug with feature naming
  • Improve bamSitesToWig modularity
  • Move large files to separate host site

[0.8.4] -- 2019-01-03

Changed

  • Switched to samblaster for default deduplication
  • Improved readability of reported results
  • Improved help messages
  • Fix mitochdonrial counting and remainding removal
  • Use gunzip instead of zcat for MacOS compatibility

Added

  • Report total mapped and unmapped reads
  • Add website docs
  • Zip unmapped files
  • Add --lite option to minimize size of output directory

[0.8.3] -- 2018-10-04

Changed

  • Fixed a bug the provided annotation file not passing the full path when called
  • Fixed a bug with a call to a non-initialized variable when missing an annotation file
  • Fixed a bug with mm9/mm10 annotation files not matching refgenie naming conventions
  • Changed how FRiF is plotted and displayed

[0.8.2] -- 2018-09-20

Changed

  • Fixed a bug with bamQC.py not employing updated pararead logger use
  • Fixed a bug with container not having all required components
  • Fixed a bug where output parent directory was not required

[0.8.1] -- 2018-09-19

Changed

  • Fixed a bug with prealignments' named pipe conflict

[0.8.0] -- 2018-09-18

Added

  • Report NRF, PBC1, and PBC2
  • Produce bigBed formatted narrowPeak file
  • Add plotting of fractions of reads in any annotated feature
  • Add peak annotation plotting
  • Add buffered fastq repair tool

Changed

  • Fixed a bug with alignment rate reporting to prealignments
  • Speed up prealignments by leveraging SE alignment
  • Fix plotting of unaligned reads
  • Fix SE incompatibility
  • Rename output files for improved readability

[0.7.0] -- 2018-06-25

Added

  • Added containerization feature
  • Added early bowtie2 index check

Changed

  • Renamed pipeline
  • Improved summary figure reporting
  • Integrated summary results into pipeline interface

[0.6.1] -- 2017-12-15

Changed

  • Fixed a bug with paired-end reads that were not in proper pairs
  • Fixed a bug with paired-end commands

[0.6.0] -- 2017-12-14

Added

  • Single-end reads are now allowed
  • Pipeline can now accommodate .bam input files
  • Added a single-base bed file output in addition to the smoothed version

Changed

  • Fixed a bug with peak counting for fseq
  • Fixed a bug with reporting estimated library sizes
  • Fixed issues with TSS enrichment calculation that could lead to stalled jobs or excess CPU use
  • Reduced verbosity of error messages for some tools
  • Reduced amount of resources requested by default
  • Introduced requirement on pypiper v0.7

[0.5.0] -- 2017-09-13

Added

  • Added rudimentary figure reporting

Changed

  • Changed default trimmer from trimmomatic to skewer
  • Made output from several tasks less verbose to make logs cleaner
  • Fixed an issue that left behind temporary samtools files if the job was killed

[0.4.0] -- 2017-07-21

Added

  • Added fseq as a peak caller option
  • Peak caller is now specified by a command line argument (defaults to macs2)
  • Count of called peaks is now reported as a pipeline result
  • Add R and ggplot2 as requirements

Changed

  • Changed TSS plotting to use R instead of python
  • TSS plot failures no longer fail the pipeline.
  • Changed Read_type to read_type to prevent duplicate columns
  • Read trimmer is now specified in option + argument style rather than as a flag.

[0.3.0] -- 2017-06-22

Added

  • Added exact cuts calculation
  • Added command-line version display
  • Added skewer as a trimmer option
  • Uses looper 'implied columns' (from looper v0.6) to derive multiple variables from organism value

Changed

  • Generalizes decoy alignments to pre-alignments, with a new --prealignment option
  • Simplified unmapped read processing to be output by bowtie directly, improving efficiency
  • Fixed bug that hard-coded mouse genome size in for macs, and fixed pipeline interface
  • Updated to new looper pipeline interface format
  • Pipeline now requires looper v0.6 or greater
  • Improved README

[0.2.0] -- 2017-04-17

Added

  • FRiP can now be calculated based on reference peaks
  • Pipeline now reports Picard estimated library size statistic
  • Added option for pyadapt trimming
  • Added example project using 'gold standard' data
  • Added new resource package grades
  • Added preliminary 'exact cuts' scripts, but they are not yet used

Changed

  • Improved README
  • Changed filename of the TSS file
  • Reorganized structure of alignment code

[0.1.0]

Added

  • First release of ATAC-seq pypiper pipeline