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Added Funcotator excluded fields option explicitly to the M2 WDL. #5242

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merged 3 commits into from
Oct 3, 2018
Merged

Added Funcotator excluded fields option explicitly to the M2 WDL. #5242

merged 3 commits into from
Oct 3, 2018

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LeeTL1220
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  • M2 WDL has explicit optional parameter for a list of fields that should be excluded from the output.
  • Both M2 WDL files are updated.

Manually tested mutect2.wdl on local backend.

Closes #5141

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I left the unsupported funcotator.wdl alone, minus a doc change to show how to specify --exclude-field

@LeeTL1220 LeeTL1220 requested review from jonn-smith and removed request for davidbenjamin October 2, 2018 18:12
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jonn-smith requested changes Oct 2, 2018
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It looks like funcotator.wdl needs some updates pulled over still. The most obvious one is the exclude fields, but it may need to be brought up to date more substantially.

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@jonn-smith I thought we had agreed (offline) that funcotator.wdl could be left alone for this PR.

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Huh. I must have completely forgotten about that.

That's fine, then.

Can you add another issue to bring funcotator.wdl up to date?

@LeeTL1220 LeeTL1220 mentioned this pull request Oct 3, 2018
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Issue added

@LeeTL1220 LeeTL1220 merged commit e52a2d8 into master Oct 3, 2018
@LeeTL1220 LeeTL1220 deleted the ll_funcotator_exclusion_list_wdl branch October 3, 2018 01:13
EdwardDixon pushed a commit to EdwardDixon/gatk that referenced this pull request Nov 9, 2018
@LeeTL1220 @EdwardDixon
Added Funcotator excluded fields option explicitly to the M2 WDLs. (b…
86d7474 
…roadinstitute#5242)

- M2 WDL has explicit optional parameter for a list of fields that should be excluded from the output.
- Both M2 WDL files are updated.

Manually tested mutect2.wdl on local backend.

Closes broadinstitute#5141
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