fulcrumgenomics/dagr

Issues

• There may be a deadlock in the task scheduler that freezes or slows pipeline execution

  #401 opened 3 years ago by clintval
  0

• TaskManager states cores used as a fraction with floating point error

  #323 opened 4 years ago by clintval
  0

• Why does Dagr use the physical processor count instead of logical for Macs only?

  #370 opened 4 years ago by clintval
  1

• API should not allow mixins between VariableResources and FixedResources

  #371 opened 5 years ago by clintval
  3

• dagR back door analysis

  #383 opened 4 years ago
  0

• Back door paths analysis

  #382 opened 4 years ago
  7

• CPU and memory resource detection should be Docker container aware.

  #377 opened 5 years ago by jacarey
  1

• Improve performance of flatMap in ScatterGather

  #363 opened 5 years ago by nh13
  0

• Empty tasks

  #355 opened 5 years ago by nh13
  5

• New Tasks

  #354 opened 5 years ago by averagehat
  1

• Move to mill

  #349 opened 6 years ago by nh13
  0

• trimming status of input fastqs for FastqToBam

  #343 opened 6 years ago by basesLoaded
  0

• I want to know all the inputs and outputs produced by the pipeline, and who made them

  #317 opened 7 years ago by nh13
  0

• Improve the documentation of Dagr

  #303 opened 8 years ago by nh13
  0

• What should PicardMetricsTask do when the prefix is None and the input file is stdin?

  #302 opened 8 years ago by nh13
  0

• Idea: run multiple independent pipelines simulataneously

  #301 opened 8 years ago by nh13
  0

• Scatter/gather tasks cannot depend upon each other

  #300 opened 8 years ago by nh13
  0

• Add new pipelines to execute while dagr is running.

  #296 opened 8 years ago by nh13
  0

• In interactive mode dagr should write the non-interactive log output to a log file in the log dir

  #272 opened 8 years ago by tfenne
  0

• A task can run even if dependent tasks fail

  #290 opened 8 years ago by nh13
  1

• Pipeline logging should describe how the status of all tasks

  #288 opened 8 years ago by nh13
  0

• Switch to scala 2.12 or enbable building and publishing for both 2.11 and 2.12

  #247 opened 8 years ago by tfenne
  6

• Improve default behaviour for @arg(minElements)

  #240 opened 8 years ago by tfenne
  0

• NullPointerException when using an empty command line argument

  #232 opened 8 years ago by nh13
  0

• Specify the maximum # of concurrent tasks or file handles as a resource type

  #230 opened 8 years ago by nh13
  0

• Support faster dependency resolutions

  #228 opened 8 years ago by nh13
  0

• Support URL in command line options

  #226 opened 8 years ago by nh13
  0

• Command line options should indicate that they are collections

  #158 opened 8 years ago by nh13
  1

• In interactive mode show the output directory (if defined) somewhere in the display.

  #224 opened 8 years ago by tfenne
  0

• Have dagr write exit code or completion status to the log file.

  #223 opened 8 years ago by nh13
  0

• Problem when trying to run ExamplePipeline on laptop

  #216 opened 8 years ago by yfarjoun
  2

• Support case classes in constructor arguments to group options for re-use.

  #212 opened 8 years ago by nh13
  0

• Log scheduled resources for a task when started.

  #208 opened 8 years ago by nh13
  0

• Modify individual tasks in a pipe chain

  #207 opened 8 years ago by nh13
  0

• Time for a 0.1.1 release?

  #201 opened 8 years ago by nh13
  2

• Sonatype release includes all transitive dependencies of picard and htsjdk

  #127 opened 8 years ago by tfenne
  1

• Support clearing an argument of type Option[String] that has a default value

  #191 opened 8 years ago by nh13
  1

• Child tasks of ParallelHaplotypeCaller should have the interval(s) in their name

  #195 opened 8 years ago by nh13
  0

• Errors for omitting require arguments should not use prefix 'UserException'

  #126 opened 8 years ago by tfenne
  0

• Run a CWL or print a CWL.

  #176 opened 8 years ago by nh13
  0

• Dagr dashboard

  #175 opened 9 years ago by nh13
  0

• Dagr can shutdown and restart

  #174 opened 9 years ago by nh13
  0

• The MarkDuplicates task should take more than one BAM as input.

  #149 opened 9 years ago by nh13
  1

• Support MarkDown in the various argument and tool usage annotations

  #172 opened 9 years ago by nh13
  1

• Freebayes vcffirstheader moved in vcflib

  #167 opened 9 years ago by nh13
  0

• Should task append to their logs?

  #154 opened 9 years ago by nh13
  1

• Display the exception when in interactive mode

  #151 opened 9 years ago by nh13
  0

• sopt never displays full sub-command descriptions

  #133 opened 9 years ago by tfenne
  0

• Better documentation on CalculateDownsamplingProportion

  #128 opened 9 years ago by nh13
  0

• What states can tasks be in?

  #123 opened 9 years ago by nh13
  3