Issues

• bam_left_align's ~reference_build argument?

  question
  hammerlab/biokepi#477 · Filter by author smondet opened on Jul 5, 2017
  2

• Better estimate each job's resource requirements and encode them into Biokepi as defaults

  enhancement
  hammerlab/biokepi#476 · Filter by author armish opened on Jun 26, 2017
  1

• Topiary fails to auto-detect reference genome for Varscan VCFs

  hammerlab/biokepi#475 · Filter by author armish opened on Jun 23, 2017

• MuTect2 can silently fail and output an empty VCF

  bug
  hammerlab/biokepi#471 · Filter by author ihodes opened on May 25, 2017

• Add Bfx.validate_bam

  target library
  hammerlab/biokepi#462 · Filter by author tavinathanson opened on May 2, 2017
  2

• Move more Input.t constructors into Biokepi

  enhancement
  hammerlab/biokepi#461 · Filter by author ihodes opened on May 2, 2017

• Fill in the gaps to cover the most basic needs of a bfx pipeline

  enhancementtarget library
  hammerlab/biokepi#451 · Filter by author armish opened on Apr 19, 2017

• Fix hlarp hack

  hammerlab/biokepi#447 · Filter by author hammer opened on Apr 4, 2017
  1

  

• Save JSON/CSV manifests automatically

  enhancement
  hammerlab/biokepi#444 · Filter by author tavinathanson opened on Mar 27, 2017
  1

• Cufflinks segfaults on every run

  tool-bug
  hammerlab/biokepi#442 · Filter by author tavinathanson opened on Mar 24, 2017

• Use new hg19 we host

  bug
  hammerlab/biokepi#433 · Filter by author ihodes opened on Feb 27, 2017
  1

• Implement OptiType pre-filtering step

  enhancement
  hammerlab/biokepi#426 · Filter by author tavinathanson opened on Feb 14, 2017
  3

• For tools where there is a bioconda recipe is available, use conda for install/ensure procedures

  enhancement
  hammerlab/biokepi#417 · Filter by author armish opened on Feb 8, 2017
  

• Make generalizable HTML manifest for Bfx.save targets

  enhancement
  hammerlab/biokepi#415 · Filter by author ihodes opened on Feb 6, 2017

• Add FastqScreen

  enhancement
  hammerlab/biokepi#408 · Filter by author ihodes opened on Jan 31, 2017

• Installing igvxml.0.0.6 fails in test example

  hammerlab/biokepi#403 · Filter by author julia326 opened on Jan 4, 2017
  1

• Name library properly in BWA-MEM

  bug
  hammerlab/biokepi#401 · Filter by author ihodes opened on Dec 22, 2016
  2

• dbsnp for b37 decoy (and probably others) is no longer hostes by the Broad where we expect

  bug
  hammerlab/biokepi#398 · Filter by author ihodes opened on Dec 16, 2016
  1

• Add "sample_name" field to a new fastqc_result product type

  enhancement
  hammerlab/biokepi#387 · Filter by author ihodes opened on Dec 6, 2016

• Support TTFI implementation of indel_realigner for n bams

  enhancement
  hammerlab/biokepi#385 · Filter by author ihodes opened on Dec 1, 2016

• Add a fastq_of_inputs like fastq_of_input

  enhancement
  hammerlab/biokepi#384 · Filter by author ihodes opened on Nov 30, 2016

• Support InsertSizeMetrics tool from Picard

  enhancement
  hammerlab/biokepi#379 · Filter by author ihodes opened on Oct 27, 2016
  1

• Add PEAR for merging overlapping paired-end reads

  enhancementtarget library
  hammerlab/biokepi#378 · Filter by author iskandr opened on Oct 26, 2016
  2

• Add support for FusionCatcher

  target library
  hammerlab/biokepi#368 · Filter by author iskandr opened on Sep 29, 2016
  4

• Reference genomes need a new abstractions

  docquestion
  hammerlab/biokepi#365 · Filter by author ihodes opened on Sep 27, 2016
  3