Giulio Genovese
Giulio Genovese
I feel like overall WDL developers need to have some way to control that docker images be cached within the WDL. Tasks that are not scattered are likely not relevant...
It seems to me very cumbersome to ask users to think this through. Currently my WDLs have a variable: ``` String docker_registry = "us.gcr.io" ``` But I have dockers uploaded...
@mcovarr I also echo @cwhelan that the solution provided is quite cumbersome. What exactly would be the complexity in devising a solution where instead you could simply define a variable...
I have just realized that this is indeed a regression from GATK 4.0 to GATK 4.1: ``` wget https://github.com/broadinstitute/gatk/releases/download/4.0.12.0/gatk-4.0.12.0.zip unzip gatk-4.0.12.0.zip ``` Running this: ``` gatk-4.0.12.0/gatk \ Mutect2 \ -R...
@davidbenjamin thank you for your work and thank you for the clarification. Is this going to be code shared by the HaplotypeCaller as well? A lot of the analyses I...
My main issue now is that I need both a fix (or workaround) for https://github.com/broadinstitute/gatk/issues/6045 and an annotation engine that counts fragments rather than reads. What I am afraid of...
WDL version [1.0](https://github.com/openwdl/wdl/blob/main/versions/1.0/SPEC.md) does not have the as_map keyword. You will have to use the WDL version [development](https://github.com/openwdl/wdl/blob/main/versions/development/SPEC.md) which contains this new function by starting the WDL with the header:...
When you have a docker such as `us.gcr.io/broad-gatk/gatk:4.2.0.0`, while it lives in a "Google registry", there is still a special bucket associated with it (and you can set Requester Pays...
I honestly have not really pulled docker images without Cromwell before, other than on my laptop for minimal testing. If I try to pull a docker manually I do get...
@aednichols I agree with your point regarding Google. However, I feel like there is a huge conflict of interest here: how can Google motivate itself to fix something that could...