TSPS-222 Updates for warp setup #203
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mmorgantaylor
changed the title
| disks: "local-disk ${disk_size_gb} SSD" | ||
| memory: "64 GiB" | ||
| memory: "${memory_gb} GiB" | ||
| preemptible: 3 |
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i would say we prob dont want preemptibles here. this is something we prob just want to run asap would be my guess unless it runs super fast (which i dont expect)
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sure, though remember this is effectively a copy of the actual test warp does, so this one will only be run manually in which case i'd think we care less about ASAP and wouldn't mind the $ savings
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i can make it an input to the wdl so that the user can decide
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yea if its comparing large vcfs most likely being preemptible wouldnt be a cost saving. being parameterized sounds good
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sounds good and i'll set the default to 0 (here and in the other one)
| --MAX_RECORDS_IN_RAM 100000 | ||
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| # compress vcf - this creates a file with .gz suffix | ||
| bgzip ~{output_basename}.liftedover.vcf |
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huh can gatk (picard) really not output a block gzipped vcf? crazy
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yeah real dumb
| memory: "~{mem_gb} GiB" | ||
| cpu: "1" | ||
| disks: "local-disk ~{disk_size} HDD" | ||
| maxRetries: max_retries |
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same thing here, do we want max_retries and preemptibles here?
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i'm fine with it since they're inputs to the wdl that can easily be overridden by the person running it
| version 1.0 | ||
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| # Liftover VCFs from hg19 to hg38 | ||
| workflow LiftoverVcfs { |
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should this be in the scientific validation folder instead? I dont think it belongs in the testing folder at least.
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yeah it sort of doesn't belong anywhere, but happy to move to scientific validation - agree that makes more sense than testing
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if you wanna be extra awesome you can add a readme to the testing folder like the other two folders in this subdir have 😄 |
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Description
Note none of this is used in the warp tests directly.
Jira Ticket
In support of work in https://broadworkbench.atlassian.net/browse/TSPS-222
Checklist (provide links to changes)