version 0.1.0

This is a maintenance release.

Full Changelog: v0.0.53...v0.1.0

v0.0.53

Bug Fixes:

• Fixes required for figure '6.1 GC Content Distribution Per Sample'. Added dependency for R library hexbin to files configure.ac and README.md, loading of library hexbin in Sample_Report.rmd.in.

• Fix required for figure '8.1 Frequency of reads in peaks'. Added a line to Sample_Report.rmd.in that renames values of the column dd to match the names of the values of the column dd (removes 'sorted.bam' from the names.).

• bug fixes provided by Pia Rautenstrauch (rautensp)

Misc:

• start using common launcher script from pigx-common.

• udate CONTRIBUTING guideline

v0.0.52

v0.0.52

v0.0.51

New features:

Differential Analysis Mode

• add optional differential analysis feature, more details in the README (https://github.com/BIMSBbioinfo/pigx_chipseq#optional-differential-analysis)

Bug Fixes :

Driver script:

• Driver script failed on settings file generated with --init (#160), fixed now

Improvements

• marking duplicates without removing is now default setting
• add bam filters to bigwig exporter (duplicate removal, mapq filtering)
• extended stats reporting with samtools stats

v0.0.43

Bug Fixes :

Settings file:

• only update app params if some are given, to solve issues like here #150

trimming rules:

• forward arguments given in the settings file to shell command

Improvements

• improve location validation from settings file
• specifiy paths of invalid files
• add distinct trimming target
• add printshellcmds to caller script

v0.0.42

Bug Fixes :

Update CLI:

• setting target 'help' and dry-run no prints help for targets

Guix:

• add Guix environment file to make creating an modifiable guix profile easier

Miscellaneous:

• do not copy report template into pigx-work directory
• simplify guix.scm by inheriting from upstream package definition

v0.0.41

Bug Fixes :

Final report:

• plot peaks samples instead of bam samples vs frip
• allow reads to map to overlapping feature for summarizeOverlaps, fixed #96

Check_Config:

• add function check_gtf_sequence_names, called inside check_fasta_header to compare sequence names of both files

idr:

• check for pairwise definition in settings file

• be more flexible in naming of the two keys

• Fixes #102

• update readme and docs

Mixed:

• trim regions out of chrom
• Fixes #40

v0.0.40

IMPROVEMENTS AND BUG FIXES

• final report: try to better guess scale factor for figure sizes based on sample numbers
• add License file

NEW FEATURES

• update final report to produce dynamic content based on analysis mode (either ATAC or ChIP)

v0.0.31

Major changes:
Spike-in adaptation
- supports multiple genome mappings
- detects Spike-in in sample sheet and maps to the genome
- creates a dict of genome indices
- main output structure changed to Mapped/[Main|Spike-in]

Minor changes:
Support for ATAC in ChiPQC report:
- Per position calculation of library complexity
- Duplication rate + Library complexity plots
dry-run performance boost
- addresses #115

v0.0.21

• guix.scm: unfix pandoc
• Fix small issue with multiQC, where output has to
• Add all wildcards to log files to satisfy snakemake
• Fix issue that occured when additional content was written to bowtie
• Update settings.yaml.in