nf-core/phaseimpute

Issues

• Check adherence to guidelines for pipeline release

  #121 opened 3 months ago by atrigila
  0

• Improve writing

  #113 opened 4 months ago by LouisLeNezet
  1

• Contribute back to NF-Core

  #112 opened 4 months ago by LouisLeNezet
  0

• Add QUILT2

  #116 opened 4 months ago by atrigila
  0

• Version ready for review v0.99.0

  #37 opened 3 months ago by LouisLeNezet
  1

• Panel chunking

  #95 opened 5 months ago by LouisLeNezet
  3

• Add tests with dog data

  #120 opened 3 months ago by atrigila
  0

• change panel.csv

  #114 opened 4 months ago by atrigila
  0

• include downsampleToCov

  #115 opened 3 months ago by atrigila
  0

• Use nft-vcf

  #106 opened 3 months ago by LouisLeNezet
  0

• Impute vcf files / snp chip array

  #108 opened 4 months ago by LouisLeNezet
  0

• Impute in batch or individually

  #107 opened 4 months ago by LouisLeNezet
  0

• Support for both CRAM and BAM at the same time

  #99 opened 5 months ago by LouisLeNezet
  1

• Add support to nf-co2footprint

  #35 opened 7 months ago by LouisLeNezet
  0

• Move to nf-schema

  #34 opened 7 months ago by LouisLeNezet
  0

• Run full scale test

  #38 opened 4 months ago by LouisLeNezet
  3

• chr check does not work on dog datasets

  #98 opened 4 months ago by atrigila
  2

• Remove POSFILE_PREPARE_GAWK

  #104 opened 4 months ago by atrigila
  0

• Update all nf-core tools

  #89 opened 5 months ago by LouisLeNezet
  0

• Move BCFTOOLS convert to vcf extract

  #80 opened 5 months ago by LouisLeNezet
  1

• Simplify csv subworkflow generation

  #70 opened 5 months ago by LouisLeNezet
  0

• Fasta fai and doc

  #94 opened 5 months ago by LouisLeNezet
  0

• Future improvement

  #90 opened 5 months ago by LouisLeNezet
  0

• Add a small test dataset with another species

  #83 opened 5 months ago by atrigila
  0

• Update metromap to match pipeline version

  #36 opened 5 months ago by LouisLeNezet
  0

• MULTIQC report per sample

  #82 opened 5 months ago by atrigila
  0

• test profile does not run quilt

  #87 opened 6 months ago by matthdsm
  1

• Make split the bam into the region specified optional

  #81 opened 6 months ago by atrigila
  0

• Add required arguments as external params to start the pipeline

  #52 opened 6 months ago by atrigila
  5

• add test for --chunks

  #63 opened 6 months ago by atrigila
  0

• design tests for each --step and --param

  #77 opened 6 months ago by atrigila
  0

• Make validate step autonomous if sites given

  #76 opened 6 months ago by LouisLeNezet
  0

• Handle --posfile param for --step impute (all tools)

  #73 opened 6 months ago by atrigila
  0

• Allow --panel param for --step impute

  #72 opened 6 months ago by atrigila
  0

• hap_legend for quilt

  #69 opened 6 months ago by atrigila
  0

• create csv files from each step

  #62 opened 6 months ago by atrigila
  0

• Add test for phasing panel

  #53 opened 6 months ago by atrigila
  1

• add validation for stitch

  #64 opened 6 months ago by atrigila
  1

• simplify posfile generation and processing

  #57 opened 6 months ago by atrigila
  0

• error with --step simulate,impute and --tools stitch

  #61 opened 6 months ago by atrigila
  1

• Add nf-test to the pipeline

  #43 opened 6 months ago by LouisLeNezet
  0

• Rewrite GLIMPSE1 subworkflow to use the panel preparation

  #55 opened 6 months ago by LouisLeNezet
  0

• Add --chunks param for --step impute

  #59 opened 6 months ago by atrigila
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• Check mandatory params for each step

  #60 opened 6 months ago by atrigila
  0

• Include glimpse2 imputation tool

  #39 opened 6 months ago by atrigila
  0

• Uniformize tools name

  #42 opened 6 months ago by LouisLeNezet
  0

• Allow binary ref creation

  #46 opened 7 months ago by atrigila
  0

• Add glimpse2 chunking method

  #45 opened 7 months ago by atrigila
  0

• Separate get panel into subworkflows

  #41 opened 7 months ago by atrigila
  0

• Select two tools at the same time

  #33 opened 7 months ago by atrigila
  0