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CNV OncotateSegments does not expose bootDiskInGb runtime parameter #3566

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LeeTL1220 opened this issue Sep 11, 2017 · 4 comments
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CNV OncotateSegments does not expose bootDiskInGb runtime parameter #3566

LeeTL1220 opened this issue Sep 11, 2017 · 4 comments
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@LeeTL1220
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This is often needed since the docker image is big.

Expose this parameter with a 20GB value
@LeeTL1220 LeeTL1220 self-assigned this Sep 11, 2017
@samuelklee
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@LeeTL1220 We'll need to add Oncotator back to the ModelSegments at some point, correct?

@LeeTL1220
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@samuelklee Yes, ASAP, we cannot support our internal TAG use cases without it.

@samuelklee
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OK. The only issue I see is converting from ModelSegments output back to the old column headers. I'd rather not have Java code for this if we can take care of it on the Oncotator side. Or perhaps even just a bash one-liner in the WDL.

@LeeTL1220
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@samuelklee Fine by me

samuelklee added a commit that referenced this issue Feb 15, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
6344ad7
samuelklee added a commit that referenced this issue Feb 15, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
1afc65d
samuelklee added a commit that referenced this issue Feb 15, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
ceb97d6
samuelklee added a commit that referenced this issue Feb 21, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
2b062c2
@samuelklee samuelklee mentioned this issue Feb 21, 2019
Merged
samuelklee added a commit that referenced this issue Feb 21, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
859b1ec
samuelklee added a commit that referenced this issue Feb 27, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
957053e
samuelklee added a commit that referenced this issue Feb 27, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
e259395
samuelklee added a commit that referenced this issue Feb 27, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
0c396b9
samuelklee added a commit that referenced this issue Feb 27, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
7e91b59
samuelklee added a commit that referenced this issue Mar 2, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
994e987
samuelklee added a commit that referenced this issue Mar 4, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
1aa4a78
samuelklee added a commit that referenced this issue Mar 4, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
06ab62d
samuelklee added a commit that referenced this issue Mar 7, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
61c5941
samuelklee added a commit that referenced this issue Mar 8, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
9c755ba
samuelklee added a commit that referenced this issue Mar 9, 2019
@samuelklee
Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)
54e7e2e
samuelklee added a commit that referenced this issue Mar 12, 2019
@samuelklee
Added some fixes for minor CNV issues. (#5699)
a6c89de 
* Cleaned up intermediate files in gCNV WDL and fixed miscellaneous typos. (#5382)

* Added output of MAD values as floats in somatic CNV WDL. (#5591)

* Exposed boot disk space for Oncotator in somatic CNV WDL. (#3566)

* Added check to skip outlier truncation if number of matrix elements exceeds Integer.MAX_VALUE in CreateReadCountPanelOfNormals. (#4734)

* Miscellaneous boy scout activities.

* Fixed some issues concerning intervals in DetermineGermlineContigPloidy documentation.

* Fixed non-kebab-case argument in CollectAllelicCountsSpark and other minor issues.

* Improved consistency of style and input/output validation across CNV tools. (#4825)
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