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# nf-core/hic: Changelog
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
* Move some options to camel_case
* Update conda environment file
* Update python scripts for python3
### `Fixed`
* Fix a bug in rm_dup in file sorting
### `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
* Support 'N' base motif in restriction/ligation sites
* Support multiple restriction enzymes/ligattion sites (comma separated) ([#31](https://github.com/nf-core/hic/issues/31))
* Add DOI ([#29](https://github.com/nf-core/hic/issues/29))
* Update manual ([#28](https://github.com/nf-core/hic/issues/28))
* Fix bug for reads extension _1/_2 ([#30](https://github.com/nf-core/hic/issues/30))
## v1.0 - [2019-05-06]
Initial release of nf-core/hic, created with the [nf-core](http://nf-co.re/) template.
### `Added`
First version of nf-core Hi-C pipeline which is a Nextflow implementation of
the [HiC-Pro pipeline](https://github.com/nservant/HiC-Pro/).
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.
* 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](https://higlass.io/)
* Quality report based on HiC-Pro MultiQC module