CHANGELOG.md



To find the state of this project's repository at the time of any of these versions, check out the tags.


nf-core/hic: Changelog
The format is based on Keep a Changelog
and this project adheres to Semantic Versioning.

v1.2.0dev

Added


Bump v1.2.0dev
Merge template nf-core 1.9
Move some options to camel_case
Update conda environment file
Update python scripts for python3


Deprecated


--skipMaps, --skipIce, --skipCool, --skipMultiQC are deprecated and replaced by --skip_maps, --skip_ice, --skip_cool, --skip_multiqc
--saveReference, --saveAlignedIntermediates, --saveInteractionBAM are replaced by --save_reference, --save_aligned_intermediates, --save_interaction_bam


v1.1.1

Fixed


Fix bug in tag. Remove '['


v1.1.0 - 2019-10-15

Added


Update hicpro2higlass with -p parameter
Support 'N' base motif in restriction/ligation sites
Support multiple restriction enzymes/ligattion sites (comma separated) (#31)
Add --saveInteractionBAM option
Add DOI (#29)
Update manual (#28)


Fixed


Fix bug for reads extension _1/_2 (#30)


v1.0 - [2019-05-06]
Initial release of nf-core/hic, created with the nf-core template.

Added

First version of nf-core Hi-C pipeline which is a Nextflow implementation of
the HiC-Pro pipeline.
Note that all HiC-Pro functionalities are not yet all implemented.
The current version supports most protocols including Hi-C, in situ Hi-C,
DNase Hi-C, Micro-C, capture-C or HiChip data.
In summary, this version allows :

Automatic detection and generation of annotation files based on igenomes
if not provided.
Two-steps alignment of raw sequencing reads
Reads filtering and detection of valid interaction products
Generation of raw contact matrices for a set of resolutions
Normalization of the contact maps using the ICE algorithm
Generation of cooler file for visualization on higlass

Quality report based on HiC-Pro MultiQC module