[do not merge] Imputation beagle with max retries #1506
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This reverts commit 3757137.
*pre splitting and prechunking beagle imputation inputs to lower log numbers and storage account egress --------- Co-authored-by: Jose Soto <[email protected]>
…istic (#1285) * remove multi sample vcf index workflow input and add it to the PreSplitVcf task. add seed number so that beagle is always deterministic. add comment to cpu input for PhaseAndImputeBeagle task * change output_callset_name to output_base_name and remove optional outputs * change n_failed_chunks ticket to an int --------- Co-authored-by: Jose Soto <[email protected]>
* clean up wdl with stuff from TSPS-241 * try to make fail fast work with double nested scatters --------- Co-authored-by: Jose Soto <[email protected]>
…ng imputation against it (#1296) * add optional error count override for testing * rename reference base prefix variable and make it more user friendly --------- Co-authored-by: Jose Soto <[email protected]>
* try auto specifying chr at end of basename * both tasks * add liftovervcfs to dockstore * allow specifying max mem
* try creating bed files * try again * try again again * a different thing * use bedtools and bed ref panel files * oops update the correct task * fix * use the right freaking file name * remove comment
update ImputationBeagle
* add array imputation quota consumed wdl * add changelogs for imputation array related workflows --------- Co-authored-by: Jose Soto <[email protected]>
* changes to help beagle imputation wdl run on a 400k sample reference panel --------- Co-authored-by: Jose Soto <[email protected]> * remove create imputation ref panel beagle wdl and changelog * PR feedback --------- Co-authored-by: Jose Soto <[email protected]> Co-authored-by: M. Morgan Aster <[email protected]>
Co-authored-by: Jose Soto <[email protected]>
…nel (#1468) * remove tasks for recovering variants not in the reference panel and separate out beagle tasks from imputation tasks * remove prechunk wdl and references to it remove "Beagle" from task names in BeagleTasks.wdl --------- Co-authored-by: Jose Soto <[email protected]>
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