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Published July 9, 2020 | Version 1.2.0
Software Open

nf-core/hic: nf-core/hic v1.2.0

Authors/Creators

  • 1. Institut Curie
  • 2. Boehringer Ingelheim
  • 3. Science for Life Laboratory
  • 4. @SciLifeLab | Karolinska Institutet

Description

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

Files

nf-core/hic-1.2.0.zip

Files (194.9 kB)

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md5:5fc20648fd2733e5f4a22ed559883b0a
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Additional details

Related works

Is supplement to
https://github.com/nf-core/hic/tree/1.2.0 (URL)