Fix running without any MELT inputs #6
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TedBrookings
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Jun 30, 2020
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Other than the typo I found, this looks straightforward.
My only other suggestion is that if we want to run without ref_std_melt_vcfs, I suppose it's possible we might want to do the same without manta or wham, so logically, similar changes could be made e.g. on line 582 and 583. In actuality, I don't think we'll ever do that, but I figured it's worth considering and explicitly rejecting (or explicitly punting for now).
wdl/GATKSVPipelineSingleSample.wdl
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| runtime_attr_override=runtime_attr_filter_vcf_by_id | ||
| } | ||
| } | ||
| if (use_melt) { |
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Suggested change
| if (use_melt) { | |
| if (use_delly) { |
Typo?
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Whoops, thanks for pointing that out!
|
At this point I don't think we envision turning off manta or wham inputs, so I'm inclined not to add extra complexity around handling that, until it becomes a thing. |
VJalili
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Update Dockerfile
knathamuni
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This fixes some points in the WDL which were failing when run with
use_meltset to false and no melt inputs provided for the reference panel.Also added an input JSON file to demonstrate how to run without MELT, which will likely be the most frequent use case when the pipeline is deployed to Terra.