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CHANGELOG.md

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nf-core/hic: Changelog

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

v2.1.0 - 2023-06-01

Added

  • Added public_aws_ecr profile for using containers stored on ECR.

Fixed

v2.0.0 - 2023-01-12

Added

  • DSL2 version of nf-core-hic pipeline
  • Add full test dataset (#80)
  • Replace local modules by the cooler nf-core module

Fixed

  • Fix error in the Arima preset (#127)

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

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