EGA-archive/beacon2-ri-tools-v2

Issues

• Annotation of VCF in beacon2-ri-tools-v2

  #25 opened 6 months ago
  3

• Validation of data as part of beacon2-ri-tools-v2

  #24 opened 5 months ago
  1

• phenopackets as entry file

  #23 opened 6 months ago
  1

• Resources (CPU, Memory) collapse when converting millions of variants

  #22 opened 7 months ago
  1

• Get total number of variants of vcf automatically

  #21 opened 8 months ago
  0

• Option to process a VCF indicating different positions with a bed file

  #20 opened 8 months ago
  1

• Option to process a VCF indicating different positions with a bed file

  #19 opened 8 months ago
  0

• Rise error when the variable does not follow the ontology structure

  #18 opened 5 months ago
  1

• Create image for the repository

  #17 opened 4 months ago
  1

• The ref allele and alt allele are changed (e.g. c>t should be t>c)

  #16 opened 7 months ago
  1

• Full format of genomicHGVSId 'NM_004006.2:c.4375C>T' (see https://hgvs-nomenclature.org/stable/background/simple/)

  #15 opened 7 months ago
  1

• We don't want (error) structural variants

  #14 opened 7 months ago
  1

• No option to have different vcf.gz files in the files_to_read folder.

  #13 opened 7 months ago
  1

• Specify in github, if the vcf needs to be vcf or vcf.gz

  #12 opened 7 months ago
  1

• Explain which folders can the user put their data? Or create another folder (with volume) specifing that is for input data (input_docs)

  #11 opened 7 months ago
  1

• When the registries are 0 (also for example when you don't have any data, only headers), specify another thing rather than Successfully. eg. Failed to convert...

  #10 opened 7 months ago
  1

• Option to parse all the different collections at the same time (specify it in the conf.py file)

  #9 opened 8 months ago
  0

• Rise error when the ALL the required variables in a collection are not fullfilled

  #8 opened 7 months ago
  1

• When having more registries than the file has, say the number of empty documents

  #7 opened 7 months ago
  1

• Volume a csv folder inside the container

  #6 opened 7 months ago
  1

• Not necessary the docker cp commands

  #5 opened 7 months ago
  1

• Add sudo in front of commands in github. To let the user only copy the commands?

  #4 opened 7 months ago
  0

• Image name in the repo is 'beacon2-ri-tools-v2_beacon-ri-tools-v2'

  #3 opened 4 months ago
  1

• In the installation guide, add the git clone command before

  #2 opened 6 months ago
  0

• Volumes, paths to where output/input folders for files are

  #1 opened 7 months ago
  1