mskcc/roslin-variant

Issues

• identical agilent v3 and v4 resources

  #345 opened 4 years ago by anoronh4
  0

• Example missing

  #341 opened 5 years ago by exic
  2

• Last cwltool release with Python 2.7 support: 2020-01-01

  #267 opened 5 years ago by mr-c
  1

• Build script ignores keyboard interrupt

  #260 opened 5 years ago by nikhil
  1

• Facets image does not have fonts on axes labels

  #335 opened 5 years ago by timosong
  1

• Toil should symlink files instead of copying them

  #317 opened 5 years ago by nikhil
  0

• Upgrade doFacets and geneLevel in Roslin

  #297 opened 5 years ago by ckandoth
  2

• ngs-filters

  #310 opened 5 years ago by nikhil
  0

• roslin-qc

  #312 opened 5 years ago by nikhil
  0

• tabix

  #313 opened 5 years ago by nikhil
  0

• remove-variants

  #311 opened 5 years ago by nikhil
  0

• vcf2maf

  #314 opened 5 years ago by nikhil
  0

• Conpair

  #304 opened 5 years ago by nikhil
  0

• basic-filtering

  #305 opened 5 years ago by nikhil
  0

• bcftools

  #306 opened 5 years ago by nikhil
  0

• snp-pileup

  #308 opened 5 years ago by nikhil
  0

• facets

  #309 opened 5 years ago by nikhil
  0

• Add more sample-level information for display in cBioPortal

  #270 opened 5 years ago by ckandoth
  2

• roslin_request_to_yaml.py bad glob

  #322 opened 5 years ago by timosong
  0

• Run roslin-filters 2.4.2 on Roslin 2.4.1 results

  #262 opened 5 years ago by ckandoth
  2

• Calculate and add TMB into data_clinical file

  #315 opened 5 years ago by ckandoth
  0

• Retroactively fix clinical data columns for cBioPortal

  #271 opened 5 years ago by ckandoth
  0

• Run MSIsensor and add result into data_clinical

  #316 opened 5 years ago by ckandoth
  0

• Fix roslin to handle qc/contamination when pairing with all pooled normals

  #301 opened 5 years ago by nikhil
  0

• Agilent_v4_51MB_Human using wrong bait/target files

  #307 opened 5 years ago by ckandoth
  2

• Fix case where restart requires inputs.yaml.

  #302 opened 5 years ago by nikhil
  0

• Bugfix for when sample names contain R1 and R2

  #279 opened 5 years ago by allanbolipata
  1

• Commits from 2.4.x that 2.5.x must absorb

  #273 opened 5 years ago by ckandoth
  3

• Make sure Toil cleans up after itself, and zip up logs

  #285 opened 5 years ago by allanbolipata
  1

• Ability to use human+mouse hybrid reference (Optional)

  #286 opened 5 years ago by allanbolipata
  1

• Add cDNA contamination files to copy_outputs.json

  #282 opened 5 years ago by allanbolipata
  0

• Add support for 1 new IMPACT and 3 new WES assays (3ec29bf and ec73c7b)

  #275 opened 5 years ago by allanbolipata
  0

• Disable calculate_abra_ram_size() in roslin_request_to_yaml.py. Always use 42GB in CWL and also in java -Xmx during execution

  #278 opened 5 years ago by allanbolipata
  0

• Stop creating fillout MAFs since we don't do group fillout

  #281 opened 5 years ago by allanbolipata
  1

• Add DMP-BAMs to inputs.yaml

  #268 opened 5 years ago by allanbolipata
  0

• Add PDXs to inputs.yaml

  #269 opened 5 years ago by allanbolipata
  0

• Increase ramMin for some tools

  #280 opened 5 years ago by allanbolipata
  1

• Update package requirements for vulnerability issues

  #287 opened 5 years ago by allanbolipata
  0

• Fix internal Jenkins testing

  #290 opened 5 years ago by nikhil
  0

• Use conpair with H and without H in Roslin

  #265 opened 5 years ago by ckandoth
  1

• Minor updates for post-pipeline scripts

  #272 opened 5 years ago by ckandoth
  1

• Default curated BAM list must be WES

  #276 opened 5 years ago by allanbolipata
  2

• Add option to specify portal_repo_path in analysis_helper and fix related bug

  #283 opened 5 years ago by allanbolipata
  1

• Add option to override stable_id in analysis_helper

  #284 opened 5 years ago by allanbolipata
  1

• Quality/coverage thresholds for gatk_find_covered_intervals in module-2

  #277 opened 5 years ago by allanbolipata
  1

• Roslin 2.4.2 with a human+mouse merged reference

  #264 opened 5 years ago by ckandoth
  2

• Delly container bug

  #266 opened 5 years ago by allanbolipata
  0

• Fix node installation

  #258 opened 5 years ago by nikhil
  0

• Singularity containers run host binaries when run in a python virtualenv

  #259 opened 5 years ago by nikhil
  0

• Optimize Abra parameters for somatic calling

  #263 opened 5 years ago by ckandoth
  0