Issues

• Fix importFile documentation

  BD2KGenomics/toil-scripts#480 · Filter by author cket opened on Feb 18, 2017
  

• Pass job to germline docker call fuctions

  in progress
  BD2KGenomics/toil-scripts#478 · Filter by author jpfeil opened on Nov 24, 2016
  

• Fix ADAM/GATK pipeline input errors

  BD2KGenomics/toil-scripts#471 · Filter by author jpfeil opened on Oct 12, 2016

• GATK Pipeline Validation Testing

  BD2KGenomics/toil-scripts#470 · Filter by author alex-hancock opened on Oct 11, 2016
  3

  

• Make sure stdout and stderr from tools are not suppressed in worker log

  BD2KGenomics/toil-scripts#466 · Filter by author hannes-ucsc opened on Sep 17, 2016
  

• Request: Accept cram input to toil-exome

  enhancement
  BD2KGenomics/toil-scripts#444 · Filter by author Jeltje opened on Sep 8, 2016

• Wrap ADAM pipeline calls in logged timers

  spark/adam
  BD2KGenomics/toil-scripts#435 · Filter by author fnothaft opened on Sep 6, 2016
  

• change STAR outSAMunmapped argument

  BD2KGenomics/toil-scripts#433 · Filter by author hbeale opened on Sep 6, 2016

• S3 tests should be skipped if bucket can't be accessed

  bug
  BD2KGenomics/toil-scripts#429 · Filter by author fnothaft opened on Aug 31, 2016

• Eliminate config options for approximate input file size

  enhancement
  BD2KGenomics/toil-scripts#427 · Filter by author hannes-ucsc opened on Aug 24, 2016

• Support germline joint genotyping and hard filtering

  BD2KGenomics/toil-scripts#426 · Filter by author jpfeil opened on Aug 24, 2016

• Refactor germline shared files download

  BD2KGenomics/toil-scripts#425 · Filter by author jpfeil opened on Aug 24, 2016

• Factor Docker version strings out

  BD2KGenomics/toil-scripts#424 · Filter by author fnothaft opened on Aug 24, 2016

• Add JEXL expressions to germline config

  BD2KGenomics/toil-scripts#423 · Filter by author jpfeil opened on Aug 24, 2016

• Rename check_output parameter to return_stdout

  BD2KGenomics/toil-scripts#394 · Filter by author cmarkello opened on Jul 29, 2016

• toil-bwa should throw error on wrong input

  BD2KGenomics/toil-scripts#393 · Filter by author Jeltje opened on Jul 29, 2016

• Add cloud pilot quality control workflows

  firecloudreadyspark/adam
  BD2KGenomics/toil-scripts#380 · Filter by author fnothaft opened on Jul 25, 2016
  

• All external process invocations should be logged

  BD2KGenomics/toil-scripts#379 · Filter by author hannes-ucsc opened on Jul 25, 2016

• Point at ADAM 0.20.0 RC for adam-pipeline

  spark/adam
  BD2KGenomics/toil-scripts#369 · Filter by author fnothaft opened on Jul 20, 2016
  

• Port remaining tests to unittest.TestCase

  enhancement
  BD2KGenomics/toil-scripts#368 · Filter by author hannes-ucsc opened on Jul 19, 2016

• test_upload_and_download_with_encryption gets into a rut

  bug
  BD2KGenomics/toil-scripts#367 · Filter by author hannes-ucsc opened on Jul 19, 2016 · 2.1.0
  1

• Replace PyTest in setup.py with make prepare like in Toil

  enhancement
  BD2KGenomics/toil-scripts#358 · Filter by author hannes-ucsc opened on Jul 15, 2016
  2

• Remove duplicated functions in gatk_processing

  planned
  BD2KGenomics/toil-scripts#330 · Filter by author jvivian opened on Jun 28, 2016 · 2.0.0
  1

  

• Print errors to STDERR

  BD2KGenomics/toil-scripts#319 · Filter by author Jeltje opened on Jun 24, 2016
  2

• Remove author tags from scripts

  BD2KGenomics/toil-scripts#310 · Filter by author fnothaft opened on Jun 20, 2016