uclahs-cds/pipeline-call-sSNV

Issues

• Update repository description to match standard

  #283 opened 14 days ago by nwiltsie
  1

• Add missing processes in SomaticSniper to resource configs

  #305 opened 6 months ago by tyamaguchi-ucla
  4

• single pipeline runs from BAM are currently broken

  #313 opened a month ago by sorelfitzgibbon
  0

• Update GATK to v4.6.0.0

  #311 opened 2 months ago by sorelfitzgibbon
  0

• update MuSE 2.0.4 -> 2.1.1

  #315 opened 2 months ago by sorelfitzgibbon
  0

• Update BCFtools to v1.21

  #316 opened 2 months ago by sorelfitzgibbon
  0

• Use `methods.setup_process_afterscript()` for process logs

  #301 opened 2 months ago by nwiltsie
  0

• running without a `panel of normals` now elicits a WARNING

  #308 opened 2 months ago by sorelfitzgibbon
  1

• Use `store_object_as_json` to store parameters

  #307 opened 2 months ago by nwiltsie
  0

• add VAF strip plot

  #208 opened 3 months ago by sorelfitzgibbon
  0

• Add example doc with CPU/Mem resources for very large samples

  #288 opened 8 months ago by Faizal-Eeman
  8

• Create separate workflows for each input type

  #296 opened 7 months ago by sorelfitzgibbon
  0

• Running out of memory in 'somaticsniper:convert_BAM2Pileup_SAMtools (2)'

  #255 opened 8 months ago by Alfredo-Enrique
  5

• Add option to input 2 or more VCFs for intersection.

  #273 opened a year ago by sorelfitzgibbon
  0

• Additional Benchmarking to be added to README?

  #285 opened 8 months ago by sorelfitzgibbon
  1

• Update contamination table instructions in README

  #286 opened 8 months ago by sorelfitzgibbon
  0

• Re-enable testing workflow after breaking changes

  #281 opened 9 months ago by nwiltsie
  0

• Unspecific Strelka issue with WGS Tumor-Normal Pair

  #262 opened a year ago by Alfredo-Enrique
  9

• standardize input structure

  #278 opened 10 months ago by sorelfitzgibbon
  1

• Backfill documentation for existing releases

  #276 opened 10 months ago by nwiltsie
  1

• Add CODEOWNERS

  #236 opened 10 months ago by yashpatel6
  1

• Update to GATK 4.5.0.0

  #258 opened a year ago by sorelfitzgibbon
  0

• add F8.config

  #249 opened a year ago by sorelfitzgibbon
  0

• simplifiy samples_to_process handling

  #253 opened a year ago by sorelfitzgibbon
  0

• move params.germline... out of methods.config

  #252 opened a year ago by sorelfitzgibbon
  0

• remove use_intersect_regions throughout since intersect_regions are required

  #251 opened a year ago by sorelfitzgibbon
  0

• move set_sample_params to main.nf

  #250 opened a year ago by sorelfitzgibbon
  0

• MuSE v2.0.4

  #247 opened a year ago by yashpatel6
  0

• Update broken Confluence links

  #240 opened a year ago by nwiltsie
  0

• add the customization option for users to change resources

  #224 opened a year ago by sorelfitzgibbon
  0

• Resources for single algorithm runs

  #243 opened a year ago by sorelfitzgibbon
  0

• MuSE 2.0.3

  #230 opened a year ago by yashpatel6
  0

• Add assertions for 2 and 3 tool combinations

  #238 opened a year ago by sorelfitzgibbon
  0

• Resource handling for non-uclahs-cds systems

  #228 opened a year ago by yashpatel6
  0

• update README before next release

  #210 opened a year ago by sorelfitzgibbon
  1

• Manta Fatal Error: Can't determine consensus pair orientation of read group '' in bam file

  #226 opened a year ago by maotian06
  19

• Some parameters are required even when the relevant algorithm is not being run

  #227 opened a year ago by sorelfitzgibbon
  0

• add MAF output

  #202 opened a year ago by sorelfitzgibbon
  0

• update BCFtools

  #204 opened a year ago by sorelfitzgibbon
  1

• think about structure under `intersect-BCFtools-1.17`

  #221 opened a year ago by sorelfitzgibbon
  0

• add intersection venn diagram

  #206 opened a year ago by sorelfitzgibbon
  1

• Adding a time limit for MuSE

  #220 opened a year ago by maotian06
  0

• Parameterize the VennDiagram version

  #219 opened a year ago by sorelfitzgibbon
  0

• remove `mutect2`` intervals` option

  #201 opened a year ago by sorelfitzgibbon
  6

• create canonical chrs output VCF?

  #217 opened a year ago by sorelfitzgibbon
  0

• update to BCFtools 1.18 and adjust pipeline to use auto indexing

  #212 opened a year ago by sorelfitzgibbon
  0

• move call-regions param to general param

  #205 opened a year ago by sorelfitzgibbon
  0

• The headers of the output VCFs still contain removed contigs

  #209 opened a year ago by sorelfitzgibbon
  0

• modularize the intersection process

  #200 opened a year ago by sorelfitzgibbon
  0

• add by-chr QC plot

  #207 opened a year ago by sorelfitzgibbon
  0