diff --git a/nextflow/main.nf b/nextflow/main.nf index d205d42..14c5d6e 100644 --- a/nextflow/main.nf +++ b/nextflow/main.nf @@ -9,7 +9,8 @@ ---------------------------------------------------------------------------------------- */ -params.max_memory = "100.GB" +// allow 2 retries; process_high: 72.GB * task.attempt = 216.GB +params.max_memory = "220.GB" params.max_cpus = 12 // sub-directories - only FastQC needs additional sub-dir diff --git a/nextflow/nextflow.config b/nextflow/nextflow.config index 91aee25..5928fae 100644 --- a/nextflow/nextflow.config +++ b/nextflow/nextflow.config @@ -26,8 +26,10 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } - errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } - maxRetries = 1 + // https://github.com/nextflow-io/nextflow/issues/563 + errorStrategy = { ( task.attempt <= process.maxRetries ) ? 'retry' : 'ignore' } + // errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } + maxRetries = 2 maxErrors = '-1' withLabel:process_single {