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[WIP] Enabling a complex query retry if memory on the cluster is insufficient #46

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[WIP] Enabling a complex query retry if memory on the cluster is insufficient #46

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99608b5
testing complex retry
mwang87 Jul 19, 2021
ab59e25
updating retry condition
mwang87 Jul 19, 2021
fa64060
adding note
mwang87 Jul 19, 2021
158f105
making the memory more complex
mwang87 Jul 19, 2021
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11 changes: 7 additions & 4 deletions workflow/workflow.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,14 @@ params.PYTHONRUNTIME = "python" // this is a hack because CCMS cluster does not

if(params.parallel_files == "YES"){
process queryData {
errorStrategy 'ignore'
//errorStrategy 'ignore'
time '2h'
//maxRetries 3
//memory { 6.GB * task.attempt }
memory { 8.GB }

// This enable multiple retries with increasing ram, and if this all fails, lets retire it
// https://github.com/nextflow-io/nextflow/issues/563
maxRetries 3
errorStrategy { (task.exitStatus in 137..140 && task.attempt <= maxRetries) ? 'retry' : 'ignore' }
memory { 8.GB + 12.G * task.attempt }

publishDir "$params.publishdir/msql", mode: 'copy'

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