v0.1.10

What's Changed

• Make backwards compatible by @alexg9010 in #197

Full Changelog: v0.1.9...v0.1.10

v0.1.9

What's Changed

• clean/reports by @alexg9010 in #189
• [export_tbx2bw] skip chromosomes without mapping by @alexg9010 in #193

Breaking Changes

The specification of annotation files has changed in version 0.1.9.
Before, annotation files for cpgIslands and refGenes were given via general::differential-methylation::annotation and fetched from the web if nonexistent. The web fetching has been removed and the annotation files must now be given via the locations dictionary.

For now, we are updating the given configuration to the new default settings layout, but this will not work with annotation files with relative paths, thus, in the future, we encourage users to retrieve the new default settings layout with 'pigx-bsseq --init settings'.")

Please see #196 and #195 for instructions how to fetch the annotation files.

Full Changelog: v0.1.8...v0.1.9

v0.1.8

This release transfers some functions from the pigx-common repo to this repo.

Full Changelog: v0.1.7...v0.1.8

version 0.1.7

This is a maintenance release.

Full Changelog: v0.1.6...v0.1.7

v0.1.6

Fix minor issues:
- samblaster deduplication:
- turn temp-file location from dir into simple prefix
- Update pigx-common.
- fix formating of some status messages
- tabix to bigwig:
- turn destranded data.frame into data.table
- update methylKit version requirement
- add tests/out folder to make clean routine

v0.1.5

v0.1.5

v0.1.4 stable release

Major Changes

• switch to using a PiGx common runner scrip (#168)
• regenerate sample genome from hg19 and update readme
• bismark genome prep now reruns if the given fasta changes

v0.1.3: hotfix release

- not fully tested, but confident

Addtion of bwa-meth alternative workflow

Major changes:

• addition of a parallel workflow based on bwa-meth
• addition of methylation caller methylDackel
• post-mapping analysis depends more on methylKits tabix-based database files
• layout of the differential analysis in the settings has been adapted from PiGx-RNAseq -
• differential analysis report was update with a new quality control section, more context descriptions for the figures and the functionality to identify regions of similar differential methylation (DMRs)
• add multiqc reports per pipeline branch (bismark and/or bwameth )

v0.0.10

v0.0.10