Repositories list

• eggd_vep_CEN_config

  Public
  Json configuration file for the implementation of VEP for the CEN assay.

  MIT License

  •0•1•1•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_generate_rd_wgs_workbook

  Public
  Python

  •

  MIT License

  •0•0•2•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_vep_TWE_config

  Public
  Json configuration file for the implementation of VEP for the TWE assay.

  MIT License

  •0•1•1•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_conductor_configs

  Public
  Repository of eggd_conductor app and assay config files

  0•0•3•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_vep_uranus_config

  Public
  Json configuration file for the implementation of VEP for the MYE assay.

  0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_generate_fusion_workbook

  Public
  Workbook app for fusions

  MIT License

  •0•0•0•1•Updated Mar 18, 2025Mar 18, 2025

• eggd_dias_reports_workflow

  Public
  Workflow definition for Dias reports

  0•1•1•0•Updated Mar 18, 2025Mar 18, 2025

• uranus_nf_core_mini

  Public
  A mini uranus mostly nf-core pipeline that incorporates mosdepth, cggpindel (not nf-core) and sentieon bwamem

  Nextflow

  •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_vep_helios_config

  Public
  MIT License

  •0•0•0•0•Updated Mar 18, 2025Mar 18, 2025

• eggd_generate_wgs_solid_cancer_workbook

  Public
  Python

  •

  MIT License

  •0•0•2•1•Updated Mar 18, 2025Mar 18, 2025

• eggd_001_Reference

  Public archive
  Perl

  •1•1•9•2•Updated Mar 17, 2025Mar 17, 2025

• eggd_vep_CENCNV_config

  Public
  Json configuration file for CEN CNV annotation using VEP.

  MIT License

  •0•0•1•0•Updated Mar 17, 2025Mar 17, 2025

• eggd_automatic_deletion

  Public
  automated deletion of NGS .tar files on DNAnexus

  0•0•0•1•Updated Mar 17, 2025Mar 17, 2025

• mnemosyne

  Public
  displays variants

  MIT License

  •0•0•0•0•Updated Mar 17, 2025Mar 17, 2025

• egg5_dias_CEN_config

  Public
  MIT License

  •0•2•1•0•Updated Mar 17, 2025Mar 17, 2025

• eggd_arriba

  Public
  Shell

  •0•0•0•0•Updated Mar 17, 2025Mar 17, 2025

• RD_requests

  Public
  Python

  •

  MIT License

  •1•0•0•0•Updated Mar 17, 2025Mar 17, 2025

• egg4_dias_TWE_config

  Public
  Config for the Dias TWE assay

  0•1•0•0•Updated Mar 15, 2025Mar 15, 2025

• eggd_dias_batch

  Public
  Python

  •1•1•7•0•Updated Mar 15, 2025Mar 15, 2025

• themis

  Public
  Code for internal bioinformatics team auditing

  Python

  •

  MIT License

  •0•3•2•0•Updated Mar 14, 2025Mar 14, 2025

• eggd_fusioninspector

  Public
  DNAnexus app to run FusionInspector for RNA

  solidcancer

  Shell

  •

  MIT License

  •0•2•0•0•Updated Mar 12, 2025Mar 12, 2025

• eggd_vcf_rescue

  Public
  Shell

  •

  MIT License

  •0•2•0•0•Updated Mar 12, 2025Mar 12, 2025

• dx_job_monitor

  Public
  Check if the 002 jobs completed correctly and sends notifications

  Python

  •0•1•0•0•Updated Mar 12, 2025Mar 12, 2025

• ici_reports_export

  Public
  Fetches information from completed ICI reports, reformats and deposits to local storage

  MIT License

  •0•0•1•0•Updated Mar 11, 2025Mar 11, 2025

• eggd_uranus_main_workflow

  Public
  DNAnexus Uranus workflow to support the Haem-Onc myeloid project

  0•2•2•0•Updated Mar 9, 2025Mar 9, 2025

• sc_wgs_monitoring

  Public
  Solid cancer WGS repository to monitor new files and new outputs from WGS workbooks jobs

  Python

  •

  MIT License

  •0•0•0•1•Updated Mar 6, 2025Mar 6, 2025

• eggd_generate_variant_workbook

  Public
  DNAnexus app for generating xlsx variant workbooks

  Python

  •0•3•7•0•Updated Mar 6, 2025Mar 6, 2025

• eggd_multiqc

  Public
  Shell

  •0•1•0•2•Updated Mar 5, 2025Mar 5, 2025

• automated-archiving

  Public
  Python script to monitor archiving on DNANexus

  pythondnanexus

  Python

  •0•2•4•0•Updated Mar 4, 2025Mar 4, 2025

• medicover_aws

  Public
  MIT License

  •0•0•0•0•Updated Feb 27, 2025Feb 27, 2025