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automate exome depth #506

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automate exome depth #506

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48e0e7a
untested changes - still awaiting inputs
mokaguys Sep 27, 2023
434d041
add expected RData file names
mokaguys Sep 27, 2023
e57e58f
tidy up pan numbers
mokaguys Sep 27, 2023
1cf628b
exclude VCP pan numbers that don't need CNV calling
mokaguys Sep 27, 2023
e43a852
tested ed automation for vcp1 and 2.. also fix #504
mokaguys Oct 4, 2023
cc8a966
think this relates to comments in dx run cmds
mokaguys Oct 6, 2023
3772ed0
TSO updates started
mokaguys Oct 13, 2023
363bddd
update to newer exome depth bed and PON
mokaguys Oct 16, 2023
b5bc093
changes to split up TSO runs, use latest TSO app, latest duty_csv app
mokaguys Oct 18, 2023
080c32a
corrections from code review
mokaguys Oct 18, 2023
df4842d
update samplesheet splitting function and correct error in for loop f…
mokaguys Oct 19, 2023
0db3612
add multiqc command to TSOcommands_list and echo job IDs
mokaguys Oct 19, 2023
f374fae
Merge pull request #507 from moka-guys/feature/TSOsplitting
Oct 20, 2023
58e0705
remove vcp3 exome depth and code review changes
mokaguys Oct 20, 2023
4968648
corrected samplesheet paths for TSO samplesheet splitting function
mokaguys Oct 20, 2023
6f726bd
corrected error in TSO samplesheet splitting function and removed com…
mokaguys Oct 20, 2023
fb36a6e
change testing to False
mokaguys Oct 23, 2023
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