Change log
All notable changes to this project will be documented in this file.
[0.11.2] -- 2024-01-22
Fixed
- fix fastqc path Issue #268
[0.11.1] -- 2024-01-17
Fixed
- changed PEPATACr.R to use lapply instead of sapply when converting yaml to data.table object
[0.11.0] -- 2023-12-22
Fixed
- adjusted requirements and docs for Looper 1.6.0, Pipestat v0.6.0, and Pypiper 0.14.0
Changed
- pipeline uses MACS3 instead of MACS2
- output schema is now a pipestat compatible JSON Schema
- collator now outputs with record_identifier name
summary
[0.10.5] -- 2023-07-31
Fixed
- adjusted requirements for Looper 1.4.2
[0.10.4] -- 2023-07-14
Fixed
- adjusted requirements for Looper (1.4.1 and above) and Eido (0.2.0 and above)
[0.10.3] -- 2021-11-23
Added
- Customize java settings in the configuration file
Changed
- Change handling of prealignment arguments
- Update handling of blacklist when using HMMRATAC
[0.10.2] -- 2021-11-01
Changed
- Update conda environment file
- Update conda docs
[0.10.1] -- 2021-10-25
Changed
- Update dockerfile for changes to R package installations
- Update bulker crate for new rpipe container
- Update tutorial docs
[0.10.0] -- 2021-07-20
Changed
- Make refgenie optional
- Use looper refgenie populate plugin to integrate refgenie
- Update docs to reflect changes to refgenie requirement and installation
- Fix file.path in reducePeaks() and take sample name argument
- Update blacklist reduce peaks step
- Rework CLI arguments to be fully explicit
- Update
settings in R - Update dockerfile to most recent refgenie usage and R package changes
- Reduce smaller file resource requests
Added
- Add assets descriptions and how to obtain to docs
- Add script to check native, conda, and container-based installs
[0.9.16] -- 2021-05-18
Changed
- Updated consensus peak documentation
- Reintroduced single container images and corresponding documentation
- Added minimum score and minimum overlap parameters to consensus peak generation
- Restore use of original F-seq as optional peak caller
- Updated peak calling using F-seq, HOMER, and HMMRATAC
- Updated PEPATACr package to rely less on PEPs within functions
- Move stats summary generation to R and outside of looper table
[0.9.15] -- 2021-03-03
Added
- Add PEP, count table, consensus peak generation documentation
- Add license
Changed
- Fix documentation page links
- Updated argument types case
- Added ability to adjust minimum sample count when creating consensus peaks
[0.9.14] -- 2021-02-05
Changed
- Update F-Seq to F-Seq2
- Add the option to install using conda
- Add script for easing installation of seqOutBias
- Use https for PEP schema; list alternative local PEP schema approach
[0.9.13] -- 2020-12-02
Changed
- Fix recovery mode for modified fastq repairing checks
[0.9.12] -- 2020-12-01
Changed
- Update bulker crate and version
[0.9.11] -- 2021-03-04
Changed
- Fixed error in order of argument terms for _remove_adapters()
Added
- Added documentation for using custom adapters
[0.9.10] -- 2020-09-28
Changed
- Changed looper pypi term
- Updated documentation to reflect companion software updates
[0.9.9] -- 2020-08-28
Changed
- Improve clarity of trimmed reads reporting
[0.9.8] -- 2020-06-16
Changed
- Fix summarizer file path construction
- Add minimum version requirements to required software
- Update uninformative adapter read calculation
- Update example output
- Update pause index calculation to be inflexible to depth
- Fix cFRiF y-axis
- Update cutadapt calculations to newer versions of cutadapt
- Update resource defaults
- Update requirement base versions
- Update schema
[0.9.7] -- 2020-05-26
Added
- Create assets summary for samples and project
- Add optional scaling of signal tracks
Changed
- Update to PEP 2.0 standard
- Update docs and examples
[0.9.6] -- 2020-03-31
Changed
- Fixed refgenie bowtie2 index assignment
[0.9.5] -- 2020-03-26
Changed
- Updated FRiF calculation to only account for the
count
column - Updated FRiF calculation to check if results are empty
[0.9.4] -- 2020-03-25
Changed
- Updated bowtie2 index checks to be in line with refgenie updates
[0.9.3] -- 2020-03-25
Changed
- Added checks for correct value return on cutadapt report checks
[0.9.2] -- 2020-03-25
Changed
- Updated refgenconf use from get_asset() to seek()
- Added check for bowtie2_index asset naming
[0.9.1] -- 2020-02-27
Added
- Report project counts table as a summary object
- Clean up additional uncommonly used downstream files
Changed
- Use bulker for container usage
- Update R install process
- Correct FastQC object reporting
- Updated logic for recover mode
- Default max length trimming is now none
- Change nomenclature regarding FRiF/PRiF plots
- Change TSS score nomenclature
[0.9.0] -- 2020-02-20
Added
- Add a how-to guide for configuring UMI settings
Changed
- Update mRNA contamination plots display properties to be more readable
- Update pause index plots to default to log10 histograms and update their display properties
- Use paper samples as the default output examples in the docs
[0.8.9] -- 2020-02-11
Changed
- Corrected Pct_reads_too_short calculation
- Updated mRNA and PI plots to plot on same axis across sample
- Updated minimum acceptable read length
- Produce both signal track types
[0.8.8] -- 2020-02-04
Changed
- Updated degradation ratio calculation for PE data
- Corrected Pct_reads_too_short to be percent not fraction
[0.8.7] -- 2020-02-04
Changed
- Updated degradation ratio calculation for SE data
- Fixed report_fastq to properly handle SE, non UMI data
[0.8.6] -- 2020-01-28
Changed
- Update FRiF calculation to optionally follow a priority ranked method
- Update how adapter insertion distributions are plotted to be the same for SE or PE data
- Make cutadapt the default for adapter removal
- Streamline the use of Refgenie assets
- Refgenie manages pause indicies
- Refgenie manages feature annotations
- Refgenie manages assets for mRNA contamination
- Refgenie manages seqOutBias required suffixerator indicies
- Change pause index and mRNA contamination plots to histograms
Added
- Add PRiF plot
- Require FLASH tool
- Produce sample level gene counts file as output
- Generate project level counts table including all samples X gene counts
- Report degradation metric for library quality
- Add BiocProject integration
[0.8.1] -- 2019-07-15
Changed
- Fix fraction in feature calculation
- Fix library complexity calculation for PE data
- Require fastq_pair tool
- Require cutadapt for SE processing
Added
- Add QC plot for adapter insertion distribution
[0.8.0] -- 2019-07-10
Changed
- Update pause index calculation and required annotation files
- Update mRNA contamination required annotation files
- Move fastq processing to separate function
- Change handling of PE data
- Update TSS profiling
Added
- Add modified fastq_pair tool to handle PE data properly
- Add pause index plotting
- Add mRNA contamination calculation and plotting
- Add fragment length distribution plotting for PE data
[0.7.3] -- 2019-06-13
Changed
- Fix missing gt in container
- Fix mappability bug with new refgenie
[0.7.2] -- 2019-06-13
Changed
- Fix --new-start bug
- Fix container libgsl library
- Adjust seqOutBias usage and flexibility
[0.7.1] -- 2019-06-12
Changed
- Update to new refgenie usage
- Update container
[0.7.0] -- 2019-06-11
Changed
- Fix multiple input file handling
- Update preseq calculation and plotting and handle small samples
- Fix TSS plotting and score calculation
- Include bedtools in required software
Added
- Add project level library complexity summarizer
- Add docs
- Add container
- Add small test example
[0.6.0] -- 2019-06-04
Changed
- Use PEPPRO R package for QC plotting and analysis
- Default uses intermediate read files to produce a deduplicated and non-deduplicated aligned BAM file
- Check for cutadapt version for multicore processing
- Update bigWig production to be variable step formatted wig
Added
- Handle GRO-seq data as input
- Created and included a PEPPRO R package for standard functions
- Add preseq requirement and plot library complexity curve
- Calculate and report read depth
- Calculate and report the percent of adapter contamination
- Produce fraction of reads in features plot
[0.5.1] -- 2019-05-09
Changed
- Simplify and clarify prealignment steps
Added
- Perform a pre-check that all required tools are callable