This pull request addresses issue #585. The LocalizeReads task was introduced to GatherSampleEvidence to simplify cases for CRAMs sourced from requester-pays and multi-regional buckets to simplify the code, but could be skipped in some cases for some cost and time savings. An optional boolean variable set to a default value of true to run LocalizeReads was added. When set to false, the LocalizeReads task is skipped.
This passed validation with both womtool and cromshell against the reference panel. The input in the json was changed to both True and False and ran as expected in both scenarios.
This pull request addresses issue #585. The LocalizeReads task was introduced to GatherSampleEvidence to simplify cases for CRAMs sourced from requester-pays and multi-regional buckets to simplify the code, but could be skipped in some cases for some cost and time savings. An optional boolean variable set to a default value of true to run LocalizeReads was added. When set to false, the LocalizeReads task is skipped. This passed validation with both womtool and cromshell against the reference panel. The input in the json was changed to both True and False and ran as expected in both scenarios.