BD2KGenomics/toil-lib

Issues

• Add DECA method in toil_lib.tools.spark_tools

  #108 opened 7 years ago by fnothaft
  0

• ADAM recompute upgrades

  #90 opened 8 years ago by fnothaft
  0

• Add Sambama index

  #103 opened 7 years ago by fnothaft
  0

• Add two new aligners

  #102 opened 7 years ago by fnothaft
  0

• Add benchmarking mode to all tools

  #101 opened 7 years ago by fnothaft
  0

• Make docker image parametrizable for all tools

  #100 opened 7 years ago by fnothaft
  0

• Add new variant callers to benchmark against

  #97 opened 7 years ago by fnothaft
  0

• Log timings to master for GATK pipeline

  #93 opened 7 years ago by fnothaft
  0

• Add sambamba, samblaster

  #95 opened 7 years ago by fnothaft
  0

• Add support for Redwood

  #69 opened 8 years ago by jvivian
  2

• Add sort option to STAR

  #91 opened 8 years ago by jvivian
  0

• Remove docker_call

  #68 opened 8 years ago by jvivian
  3

• Add fusion results to Kallisto output

  #87 opened 8 years ago by jvivian
  0

• Revert Within KeepPairs to Within in STAR

  #85 opened 8 years ago by jvivian
  0

• return rnaSJ.out.tab for STAR

  #83 opened 8 years ago by jvivian
  0

• Support piped commands in docker_call

  #80 opened 8 years ago by glennhickey
  2

• FileIOStore symlinks don't work with docker

  #82 opened 8 years ago by glennhickey
  1

• S3IOStore cannot transfer big files

  #81 opened 8 years ago by glennhickey
  2

• Move jpfeil/oncotator:1.9 to cgl-docker-lib

  #79 opened 8 years ago by jvivian
  0

• Fix typo in rsem_postprocess

  #76 opened 8 years ago by jvivian
  0

• Remove mutable=True from toil-lib

  #74 opened 8 years ago by jvivian
  0

• Release 1.1.2

  #73 opened 8 years ago by jvivian
  0

• Update to quay.io tools in run_rsem_postprocess

  #70 opened 8 years ago by jvivian
  0

• Refactor rsem_postprocess

  #71 opened 8 years ago by jvivian
  1

• 1.1.1 Release

  #67 opened 8 years ago by jvivian
  0

• Add limitBAMsortRAM to STAR

  #49 opened 8 years ago by jvivian
  3

• not pip-installable on cgcloud toil-box-templated toil-leader?

  #65 opened 8 years ago by ArtRand
  1

• Make indel realignment optional

  #63 opened 8 years ago by jpfeil
  0

• Add mark secondary option to run_bwakit

  #61 opened 8 years ago by jpfeil
  0

• Add manual (Sphinx documentation)

  #59 opened 8 years ago by hannes-ucsc
  2

• Mock_mode prevents downloads of intermediate files

  #57 opened 8 years ago by almussel
  0

• Move Spark service jobs over from toil

  #45 opened 8 years ago by fnothaft
  1

• Use parse_version

  #55 opened 8 years ago by cket
  0

• Update all docker_call invocations to pass job

  #44 opened 8 years ago by cket
  0

• Add unit tests for tools

  #54 opened 8 years ago by cket
  0

• Convert s3am invocations to use the s3am docker image

  #38 opened 8 years ago by hannes-ucsc
  0

• Add logging for each job's disk resources used.

  #51 opened 8 years ago by arkal
  1

• Add defer to inferior filestore

  #52 opened 8 years ago by arkal
  1

• Remove usages of 'shell=True' in AWSProvisioner

  #50 opened 8 years ago by cket
  1

• Return log.final for STAR alignment

  #47 opened 8 years ago by jvivian
  0

• Write BAM validator function

  #37 opened 8 years ago by hannes-ucsc
  2

• Add QC for CKCC

  #40 opened 8 years ago by jvivian
  1

• Add Within KeepPairs to STAR

  #35 opened 8 years ago by jvivian
  0

• make pypi is broken

  #33 opened 8 years ago by jvivian
  0

• Add generate_file

  #29 opened 8 years ago by jvivian
  0

• `make pypi` fails on jenkins

  #27 opened 8 years ago by cket
  2

• Setup only allows old version of Toil

  #25 opened 8 years ago by cket
  0

• Sporadic NoSuchFileError in processFinishedJob

  #24 opened 8 years ago by hannes-ucsc
  1

• `make pypi` fails with password prompt and None type error

  #22 opened 8 years ago by hannes-ucsc
  0

• Don't push to PyPi for PR builds

  #20 opened 8 years ago by jvivian
  0