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nextflow-stack
AWS stack to run Nextflow pipelines on Batch using shared resources
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Increase GRIDSS assembly default time limit
#66
Closed
scwatts
closed
1 year ago
scwatts
commented
1 year ago
Background
the SBJ03026/L2201887 GRIDSS assembly task exceeded the default 8 hour time limit, causing it to fail
the task was automatically retried with an extended 16 hour time limit, which succeeded
in the failed first attempt, the task reached the final step of mapping breakend assembly contigs back to the ref genome
I expect the task needed less than 1-2 hours to finish
Changes
increased default time limit for GRIDSS assembly tasks from 8 hours to 12 hours
separated GRIDSS assembly task retries and avoid decreasing CPU count on retry
Background
Changes