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23 May 2024

  • updated bcftools to biocontainers/bcftools:1.20--h8b25389_0


24 Apr 2024

  • incremented data release version to 'main-programme_v18_2023-12-21'
  • ported DEFINE_COHORT module script to python and re-wrote LabKey SQL query explicitly including consent
  • added process tests to all modules
  • parameterised LSF project_code
  • changed to use default user singularity cache
  • included automated test runs in CI/CD


10 Oct 2023

  • ported from WDL/Cromwell to Nextflow DSL2
  • renamed to Structural Variant workflow
  • added configuration for both RE (Helix/HPC) and CloudRE (CloudOS)


  • New possible cohort: ca-all so that both cancer somatic and cancer germline can be queried on the same run
  • Inclusion of prevalence report (summary_geneName_sampleType.txt) for main cancer indications
  • Inclusion of MCC for CNV both germline and somatic on 100kGP genomes. Also, on somatic CNV for dragen realignments
  • CNV_pass_only option: CNV are assigned for the whole genome (some parts are neutral CN = 2). Canvas struggles to call (FILTER = PASS) focal CNVs, but removing PASS can retrieve those. Use it with care!
  • Removal of Resultsfailed files instead one single inaccessibleVCF.tsv* file list all, if any, vcf could not be accessed (probably due to permission issues, please open a ticket if it happens to you)
  • Workflow files are not organised in folders! You only need to change the and the files in the input/ dir!