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@nservant nservant released this 09 Jul 06:54
· 299 commits to master since this release
1.2.0
b84069e
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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
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