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fulcrumgenomics / dagr

A scala based DSL and framework for writing and executing bioinformatics pipelines as Directed Acyclic GRaphs
MIT License
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PicardTask to use the Intel inflater/deflater only if it is safe, by default #368

Closed clintval closed 4 years ago

clintval commented 4 years ago

Many of my Dagr pipelines now require the Intel Inflater/Deflater to be conditionally turned off across all executables that use htsjdk because of Intel-HLS/GKL#101. Can we intelligently use the Intel Inflater/Deflater, or not, on any Picard task as a default?

Followup to: https://github.com/fulcrumgenomics/dagr/pull/367 (including your comment) and https://github.com/fulcrumgenomics/fgbio/pull/534

Note: None of my recent PRs provide parameterization, or default-setting, for GATK tasks!

I have tested this using pipelines that have Picard tasks and confirm it works as expected!

codecov-io commented 4 years ago

Codecov Report

Merging #368 into master will increase coverage by 0.01%. The diff coverage is 92.52%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #368      +/-   ##
==========================================
+ Coverage   91.55%   91.56%   +0.01%     
==========================================
  Files          31       31              
  Lines        1184     1186       +2     
  Branches       81       81              
==========================================
+ Hits         1084     1086       +2     
  Misses        100      100
Impacted Files Coverage Δ
.../main/scala/dagr/core/execsystem/TaskManager.scala 90.79% <79.31%> (ø)
.../main/scala/dagr/core/execsystem/TaskTracker.scala 92.94% <93.33%> (ø)
...rc/main/scala/dagr/core/execsystem/GraphNode.scala 94.11% <100.00%> (ø)
...in/scala/dagr/core/execsystem/NaiveScheduler.scala 100.00% <100.00%> (ø)
.../main/scala/dagr/core/execsystem/ResourceSet.scala 100.00% <100.00%> (ø)
...src/main/scala/dagr/core/tasksystem/Pipeline.scala 88.88% <100.00%> (+0.88%) :arrow_up:
...ore/src/main/scala/dagr/core/tasksystem/Task.scala 95.71% <100.00%> (ø)
... and 3 more

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nh13 commented 4 years ago

@clintval this should be unblocked given fulcrumgenomics/commons#59 is merged.

clintval commented 4 years ago

@nh13 all set. Is TravisCI no longer enabled in this repository?

nh13 commented 4 years ago

Re-opening to see if I can get travis-ci to build.

nh13 commented 4 years ago

@clintval looks like it wasn't triggering, re-opening did the trick