diff --git a/workflow/workflow.nf b/workflow/workflow.nf index 2a35c90..5d3eae9 100644 --- a/workflow/workflow.nf +++ b/workflow/workflow.nf @@ -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'