combine bqsr processes into one#877
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gongyixiao merged 17 commits intodevelopfrom Aug 11, 2021
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| task.time = task.exitStatus.toString() in wallTimeExitCode ? { params.maxWallTime } : { params.medWallTime } | ||
| } | ||
| if (workflow.profile == "juno") { | ||
| if(bam.size() > 60.GB) { |
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are 60.GB and 50.GB are optimized value based on our test run?
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the logic behind this choice may be a little outdated, from when i was combining MarkDup and BQSR together. I cut the numbers from MarkDup in half to account for the fact that we were processing/writing the bam twice. I'll revert this back to what the parameters were for RecalibrateBam and then revert based on testing.
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… match the original RecalibrateBam
… enhancement/combineBQSR
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Please remove these two files |
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Adding
BQSRPipelineSparkin one process as an alternative toBaseRecalibratorandApplyBQSRin two separate processes.If the process fails twice it switches from
BQSRPipelineSparktoBaseRecalibratorandApplyBQSRin the same process for the remaining attempt(s)