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https://github.com/MillironX/nf-configs.git
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Modularised error handling strategy to per pipeline basis
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parent
c9c4d02f0d
commit
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5 changed files with 41 additions and 14 deletions
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@ -15,6 +15,14 @@
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process {
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// error and retry handling
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
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maxRetries = 2
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// process labels
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 4.GB * task.attempt, 'memory' ) }
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@ -72,3 +80,4 @@ def check_max(obj, type) {
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}
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}
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}
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@ -14,6 +14,14 @@
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// process-specific resource requirements - reduced specification from those in chipseq/conf/base.config
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process {
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// error and retry handling
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
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maxRetries = 2
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// process labels
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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@ -72,3 +80,4 @@ def check_max(obj, type) {
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}
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}
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}
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@ -14,6 +14,14 @@
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// process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config
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process {
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// error and retry handling
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
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maxRetries = 2
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// process labels
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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@ -14,8 +14,13 @@
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// process-specific resource requirements - reduced specification from those in sarek/conf/base.config
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process {
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// error and retry handling
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' }
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maxRetries = 2
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// process labels
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withLabel:process_low {
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@ -28,16 +28,6 @@ params {
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}
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// container engine
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singularity {
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enabled = true
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autoMounts = true
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}
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// hpc configuration specific to ShARC
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process {
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@ -49,9 +39,15 @@ process {
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queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
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clusterOptions = { "-l rmem=${task.memory.toGiga()}G" }
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// error and retry handling
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}
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errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
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maxRetries = 2
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// container engine
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singularity {
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enabled = true
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autoMounts = true
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}
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