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Description of the bug
During release 5.4.0, we had lots of problems with the pipeline failing on AWS.
We need to optimise it so we dont have to monitor (and burn a lot of money/energy on multiple -resumes).
This was the modification to the configuration I ended up using to ge tthe pipeine to run though:
process {
maxRetries = 2
errorStrategy = { task.exitStatus in ((130..145) + 104 + 175) ? 'retry' : 'terminate' }
withName: 'NFCORE_MAG:MAG:ASSEMBLY:LONGREAD_ASSEMBLY:FLYE' {
memory = '128.GB'
}
withName: 'ALE' {
memory = { 36.GB * task.attempt }
errorStrategy = 'ignore'
}
withName: 'PROKKA' {
errorStrategy = 'ignore'
}
}
The failing tasks that were ignored either defined by base.config or in the profile above were:
Command used and terminal output
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