Move foreign file staging after storeDir evaluation #5759
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Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
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Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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@jorgee were you able to confirm that this change fixes the reported issue? using the test case they gave? |
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@bentsherman I tested with a slightly different case where output was different from the input. I have noted the input is the same as output in the example they provided. In this case the fix is not working because when the stage dir is removed, the file in the storeDir is also removed, and nextflow downloads again because the file does not exist. |
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close #5468
This PR modifies the foreign file staging management in TaskProcessor.makeTaskContextStage2 to return the staging batch and do the staging copy just before the hash computation. It allow to skip executions in storeDir without requiring to download inputs.