diff --git a/conf/pipeline/atacseq/sbc_sharc.config b/conf/pipeline/atacseq/sbc_sharc.config index e50695c..0660591 100644 --- a/conf/pipeline/atacseq/sbc_sharc.config +++ b/conf/pipeline/atacseq/sbc_sharc.config @@ -15,6 +15,14 @@ process { + // error and retry handling + + errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' } + maxRetries = 2 + + + // process labels + withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } memory = { check_max( 4.GB * task.attempt, 'memory' ) } @@ -72,3 +80,4 @@ def check_max(obj, type) { } } } + diff --git a/conf/pipeline/chipseq/sbc_sharc.config b/conf/pipeline/chipseq/sbc_sharc.config index 60912f3..6fef3ba 100644 --- a/conf/pipeline/chipseq/sbc_sharc.config +++ b/conf/pipeline/chipseq/sbc_sharc.config @@ -14,6 +14,14 @@ // process-specific resource requirements - reduced specification from those in chipseq/conf/base.config process { + + // error and retry handling + + errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' } + maxRetries = 2 + + + // process labels withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } @@ -72,3 +80,4 @@ def check_max(obj, type) { } } } + diff --git a/conf/pipeline/rnaseq/sbc_sharc.config b/conf/pipeline/rnaseq/sbc_sharc.config index 52bf0ff..8cefa40 100644 --- a/conf/pipeline/rnaseq/sbc_sharc.config +++ b/conf/pipeline/rnaseq/sbc_sharc.config @@ -14,6 +14,14 @@ // process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config process { + + // error and retry handling + + errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' } + maxRetries = 2 + + + // process labels withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } diff --git a/conf/pipeline/sarek/sbc_sharc.config b/conf/pipeline/sarek/sbc_sharc.config index 204d73b..434b8a2 100644 --- a/conf/pipeline/sarek/sbc_sharc.config +++ b/conf/pipeline/sarek/sbc_sharc.config @@ -14,8 +14,13 @@ // process-specific resource requirements - reduced specification from those in sarek/conf/base.config process { - + // error and retry handling + + errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' } + maxRetries = 2 + + // process labels withLabel:process_low { diff --git a/conf/sbc_sharc.config b/conf/sbc_sharc.config index 20b8661..de1ab0c 100644 --- a/conf/sbc_sharc.config +++ b/conf/sbc_sharc.config @@ -28,16 +28,6 @@ params { } -// container engine - -singularity { - - enabled = true - autoMounts = true - -} - - // hpc configuration specific to ShARC process { @@ -49,9 +39,15 @@ process { queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' } clusterOptions = { "-l rmem=${task.memory.toGiga()}G" } - // error and retry handling +} - errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' } - maxRetries = 2 + +// container engine + +singularity { + + enabled = true + autoMounts = true } +