CHANGELOG.md

nf-core/hic: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.3.1 - 2021-09-25

Fixed

• Fix bug in conda environment for cooltools (#109)

v1.3.0 - 2021-05-22

• Change the /tmp/ folder to ./tmp/ folder so that all tmp files are now in the work directory (#24)
• Add --hicpro_maps options to generate the raw and normalized HiC-Pro maps. The default is now to use cooler
• Add chromosome compartments calling with cooltools (#53)
• Add HiCExplorer distance decay quality control (#54)
• Add HiCExplorer TADs calling (#55)
• Add insulation score TADs calling (#55)
• Generate cooler/txt contact maps
• Normalize Hi-C data with cooler instead of iced
• New --digestion parameter to automatically set the restriction_site and ligation_site motifs
• New --keep_multi and keep_dup options. Default: false
• Template update for nf-core/tools
• Minor fix to summary log messages in pipeline header

Fixed

• Fix bug in stats report which were not all correcly exported in the results folder
• Fix recurrent bug in input file extension (#86)
• Fix bug in --bin_size parameter (#85)
• --min_mapq is ignored if --keep_multi is used

Deprecated

• --rm_dup and --rm_multi are replaced by --keep_dups and --keep_multi

v1.2.2 - 2020-09-02

Added

• Template update for nf-core/tools v1.10.2
• Add the --fastq_chunks_size to specify the number of reads per chunks if split_fastq is true

Fixed

• Bug in --split_fastq option not recognized

v1.2.1 - 2020-07-06

Fixed

• Fix issue with --fasta option and .fa extension (#66)

v1.2.0 - 2020-06-18