CHANGELOG.md

nf-core/hic: Changelog

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

v1.3.0dev

• Add HiCExplorer distance decay quality control
• Add HiCExplorer TADs calling
• Add insulation score TADs calling
• Generate cooler/h5/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 v1.11
• Minor fix to summary log messages in pipeline header

Fixed

• 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_dup 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

Added

• Bump v1.2.0
• 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)
• 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