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automate exome depth#506

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aledj2 wants to merge 17 commits intomastermoka-guys/automate_demultiplex:masterfrom feature/exomedepthmoka-guys/automate_demultiplex:feature/exomedepthCopy head branch name to clipboard

+569-190

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Commits on Sep 27, 2023

• untested changes - still awaiting inputs

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  committed
  48e0e7a

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• add expected RData file names

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  committed
  434d041

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• tidy up pan numbers

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  committed
  e57e58f

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• exclude VCP pan numbers that don't need CNV calling

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  committed
  1cf628b

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Commits on Oct 4, 2023

• tested ed automation for vcp1 and 2.. also fix #504

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  committed
  e43a852

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Commits on Oct 6, 2023

• think this relates to comments in dx run cmds

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  committed
  cc8a966

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Commits on Oct 13, 2023

• TSO updates started

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  3772ed0

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Commits on Oct 16, 2023

• update to newer exome depth bed and PON

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  committed
  363bddd

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Commits on Oct 18, 2023

• changes to split up TSO runs, use latest TSO app, latest duty_csv app

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  b5bc093

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• corrections from code review

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  080c32a

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Commits on Oct 19, 2023

• update samplesheet splitting function and correct error in for loop for post run commands list for TSO

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  committed
  df4842d

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• add multiqc command to TSOcommands_list and echo job IDs

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  0db3612

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Commits on Oct 20, 2023

• Merge pull request #507 from moka-guys/feature/TSOsplitting

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  Aled Jones

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  f374fae

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• remove vcp3 exome depth and code review changes

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  committed
  58e0705

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• corrected samplesheet paths for TSO samplesheet splitting function

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  committed
  4968648

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• corrected error in TSO samplesheet splitting function and removed comment lines for dx run commands file

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  6f726bd

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Commits on Oct 23, 2023

• change testing to False

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  fb36a6e

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