malariagen/pipelines

Issues

• Number of SNPs and Indels doesn't match with the numbers reported in README files

  #109 opened 2 years ago by Rohit-Satyam
  4

• Add platform argument to build_pipeline_release script

  #38 opened 3 years ago by gbggrant
  2

• Repo file and folder structure

  #1 opened 3 years ago by alimanfoo
  3

• Pipeline versioning strategy

  #5 opened 3 years ago by alimanfoo
  2

• Add WDL validation CI

  #13 opened 3 years ago by alimanfoo
  1

• Define read group contents in vector short read alignment pipelines

  #27 opened 3 years ago by tnguyensanger
  1

• Input source for mosquito short read alignment pipeline

  #32 opened 3 years ago by alimanfoo
  3

• Validation/truth datasets for variant calling calibration, comparison and evaluation

  #33 opened 3 years ago by alimanfoo
  26

• Output of vector short read alignment pipeline is named *.bam.bam

  #68 opened 3 years ago by tnguyensanger
  1

• Use flexible fields in manifest

  #70 opened 3 years ago by tnguyensanger
  0

• Determine final lanelet manifest fields required for vector alignment and genotyping

  #54 opened 3 years ago by tnguyensanger
  1

• Cromwell configurations on farm5 are using localization = copy, which explodes size of workflow working directory

  #56 opened 3 years ago by tnguyensanger
  0

• Convert cram to bam in vector alignment pipeline

  #60 opened 3 years ago by tnguyensanger
  0

• malaria-dk lsf group deprecated

  #66 opened 3 years ago by tnguyensanger
  0

• Provide example crams released by Core Sequencing

  #26 opened 3 years ago by tnguyensanger
  3

• How to make bwa short read alignment deterministic for testing

  #41 opened 3 years ago by tnguyensanger
  1

• Genotype Concordance Validation of genotyping pipelines

  #45 opened 3 years ago by tnguyensanger
  10

• Create pipelines that download multiple samples from IRODS in a batch

  #52 opened 3 years ago by tnguyensanger
  0

• Minimal input to validate plumbing of vector short read pipelines

  #25 opened 3 years ago by tnguyensanger
  5

• Mosquito short read alignment pipeline - validation

  #22 opened 3 years ago by alimanfoo
  13

• Mosquito short read alignment pipeline

  #2 opened 3 years ago by alimanfoo
  5

• Mosquito phasing pipeline development

  #44 opened 3 years ago by alimanfoo
  22

• Ag3.0 phasing pipeline production run

  #80 opened 3 years ago by alimanfoo
  15

• Validate results for phasing pipeline

  #73 opened 4 years ago by hardingnj
  17

• Copy script to convert vcf to zarr to this repo

  #35 opened 4 years ago by tnguyensanger
  0

• Port baseline Plasmodium amplicon SNP calling pipeline.

  #37 opened 4 years ago by samuelklee
  1

• Update vector spec to reflect removal of calmd and usage of Picard SetNmMdAndUqTags tool

  #17 opened 5 years ago by gbggrant
  1

• Fix picards location issue for singulairty

  #15 opened 5 years ago by JonKeatley112
  0

• Mosquito short read alignment pipeline - dockerfiles

  #11 opened 5 years ago by alimanfoo
  4

• Mosquito short read alignment pipeline - test dataset

  #6 opened 5 years ago by alimanfoo
  8

• Add script to test whether people have access to Sanger Farm5

  #3 opened 5 years ago by tnguyensanger
  2