Structural variant workflow changelog¶
- 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 submit_script.sh and the files in the input/ dir!
Last update: November 20, 2023