nf-core/variantbenchmarking

Issues

• enable liftover option for test vcfs

  #113 opened a month ago by kubranarci
  0

• add plots and reports to MULTIQC

  #88 opened a month ago by kubranarci
  1

• missing chain and rename_chr files

  #112 opened a month ago by kubranarci
  0

• Can't download singularity containers for modules with `oras://`

  #110 opened a month ago by fellen31
  2

• Broken link to truth info

  #109 opened a month ago by fellen31
  1

• Extensive testing of subworkflows

  #94 opened a month ago by kubranarci
  13

• Add an test case for rat

  #102 opened 2 months ago by kubranarci
  2

• add nft-vcf

  #67 opened a month ago by kubranarci
  0

• update happy modules

  #98 opened a month ago by kubranarci
  0

• add test cases to CI

  #85 opened a month ago by kubranarci
  0

• add truth files into igenome

  #104 opened 2 months ago by kubranarci
  0

• refactoring input truth files

  #100 opened 2 months ago by kubranarci
  0

• rename bed file

  #97 opened 2 months ago by kubranarci
  0

• Detection of variant tools from vcf header

  #101 opened 2 months ago by kubranarci
  0

• Use datavzrd to create reports that are usable with NCBench

  #52 opened 2 months ago by famosab
  1

• add test case hg38 for nf-cmgg-structural

  #31 opened 8 months ago by kubranarci
  0

• generate somatic test files for COLO-829

  #93 opened 2 months ago by kubranarci
  0

• somatic workflow

  #96 opened 2 months ago by kubranarci
  0

• add oncoliner tools

  #89 opened 3 months ago by kubranarci
  0

• Release v1.0.0 requirements

  #95 opened 2 months ago by kubranarci
  0

• oncoliner assessment tool

  #92 opened 2 months ago by kubranarci
  0

• coverage stratification

  #65 opened 5 months ago by kubranarci
  0

• support for trio analysis for mendelian inheritance errors

  #82 opened 4 months ago by kubranarci
  0

• integrate module/snakemake

  #69 opened 5 months ago by kubranarci
  0

• update to nf-schema@2.0.0

  #29 opened 3 months ago by kubranarci
  0

• add nf-test

  #81 opened 4 months ago by kubranarci
  0

• pipeline test with stub

  #83 opened 4 months ago by kubranarci
  0

• design metro-map

  #62 opened 4 months ago by kubranarci
  0

• fullfill readme

  #66 opened 4 months ago by kubranarci
  0

• add liftover option for truths

  #77 opened 5 months ago by kubranarci
  0

• add aws full test

  #44 opened 5 months ago by kubranarci
  0

• add support for multi-sample files

  #71 opened 5 months ago by kubranarci
  0

• generate truth.config

  #42 opened 5 months ago by kubranarci
  0

• add SV benchmarking for somatic

  #46 opened 5 months ago by kubranarci
  1

• fix prepy + rtgtools eval comb

  #57 opened 6 months ago by kubranarci
  0

• svync process is not running through

  #32 opened 6 months ago by kubranarci
  0

• test variant-extractor for SVs

  #58 opened 6 months ago by kubranarci
  0

• wittyer bug

  #59 opened 6 months ago by kubranarci
  1

• rtgtools format takes forever

  #54 opened 6 months ago by kubranarci
  0

• plot.r fix

  #45 opened 6 months ago by kubranarci
  0

• split variant benchmarking by type

  #27 opened 6 months ago by kubranarci
  0

• add SQLite database

  #25 opened 6 months ago by kubranarci
  0

• fix wittyer

  #50 opened 6 months ago by kubranarci
  1

• fix workflow prepy

  #48 opened 7 months ago by kubranarci
  0

• somatic benchmarking

  #41 opened 7 months ago by kubranarci
  0

• add plot functions

  #28 opened 7 months ago by kubranarci
  0

• add a script to merge benchmarking results

  #35 opened 7 months ago by kubranarci
  0

• exposing benchmarking params

  #33 opened 8 months ago by kubranarci
  1

• standardization VCF filtering

  #18 opened 9 months ago by kubranarci
  5

• add vcf_preprocessing_deduplication subworkflow

  #22 opened 9 months ago by kubranarci
  0