CHANGELOG.md

# 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).

## v1.2.0dev - 2020-05-12

### `Added`

* Bump v1.2.0dev
* Merge template nf-core 1.9
* Move some options to camel_case
* Update python scripts for python3
* Update conda environment file
  * python base `2.7.15` > `3.7.6`
  * pip `19.1` > `20.0.1`
  * scipy `1.2.1` > `1.4.1`
  * numpy `1.16.3` > `1.18.1`
  * bx-python `0.8.2` > `0.8.8`
  * pysam `0.15.2` > `0.15.4`
  * cooler `0.8.5` > `0.8.6`
  * multiqc `1.7` > `1.8`
  * iced `0.5.1` > `0.5.6`
  * *_New_* pymdown-extensions `7.1`
  * *_New_* hicexplorer `3.4.3`
  * *_New_* bioconductor-hitc `1.32.0`
  * *_New_* r-optparse `1.6.6`
  * *_New_* ucsc-bedgraphtobigwig `377`
  * *_New_* cython `0.29.19`
  * *_New_* cooltools `0.3.2`
  * *_New_* fanc `0.8.30`
  * *_Removed_* r-markdown

### `Fixed`

* Fix error in doc for Arima kit usage
* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
are expected to be sorted (sort -m)

### `Deprecated`

* Command line options converted to `camel_case`:
  * `--skipMaps` > `--skip_maps`
  * `--skipIce` > `--skip_ice`
  * `--skipCool` > `--skip_cool`
  * `--skipMultiQC` > `--skip_multiqc`
  * `--saveReference` > `--save_reference`
  * `--saveAlignedIntermediates` > `--save_aligned_intermediates`
  * `--saveInteractionBAM` > `--save_interaction_bam`

## v1.1.1 - 2020-04-02

### `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](https://github.com/nf-core/hic/issues/31))
* Add --saveInteractionBAM option
* Add DOI ([#29](https://github.com/nf-core/hic/issues/29))
* Update manual ([#28](https://github.com/nf-core/hic/issues/28))

### `Fixed`

* 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.

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](https://higlass.io/)
* Quality report based on HiC-Pro MultiQC module