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FIX: Strict syntax for sage #1072

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FIX: Strict syntax for sage #1072

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90c442a
fix strict syntax
maxulysse Apr 7, 2026
f91832e
Apply suggestion from @maxulysse
maxulysse Apr 7, 2026
c45a977
Merge branch 'master' into sage
maxulysse Apr 14, 2026
60e0893
Merge branch 'master' into sage
jfy133 Apr 25, 2026
bfb36ed
Fix linting
jfy133 Apr 25, 2026
570adf7
Apply suggestion from @thomasyu888
maxulysse Apr 28, 2026
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50 changes: 22 additions & 28 deletions conf/sage.config
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
// Config profile metadata
params {
config_profile_description = 'The Sage Bionetworks Nextflow Config Profile'
config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)'
config_profile_contact = 'Rixing Xu (@rxu17)'
config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows'

// Leverage us-east-1 mirror of select human and mouse genomes
Expand All @@ -12,6 +12,9 @@ params {
max_time = 240.h
single_cpu_mem = 6.GB

// Define task exit errors
exit_status_scaling = [143,137,104,134,139,247]

warning_message = {
System.out.println("WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
System.out.println("WARNING:")
Expand Down Expand Up @@ -60,47 +63,38 @@ process {
// Enable retries globally for certain exit codes
errorStrategy = { task.attempt <= 5 ? 'retry' : 'finish' }

cpus = { 1 * factor(task, 2) }
memory = { 6.GB * factor(task, 1) }
time = { 24.h * factor(task, 1) }
cpus = { task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1 }
memory = { 6.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
time = { 24.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }

// Process-specific resource requirements
withLabel: process_single {
cpus = { 1 * factor(task, 2) }
memory = { 6.GB * factor(task, 1) }
time = { 24.h * factor(task, 1) }
cpus = { task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1 }
memory = { 6.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
time = { 24.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
}
withLabel: process_low {
cpus = { 2 * factor(task, 2) }
memory = { 12.GB * factor(task, 1) }
time = { 24.h * factor(task, 1) }
cpus = { 2 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
memory = { 12.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
time = { 24.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
}
withLabel: process_medium {
cpus = { 8 * factor(task, 2) }
memory = { 32.GB * factor(task, 1) }
time = { 48.h * factor(task, 1) }
cpus = { 8 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
memory = { 32.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
time = { 48.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
}
withLabel: process_high {
cpus = { 16 * factor(task, 2) }
memory = { 64.GB * factor(task, 1) }
time = { 96.h * factor(task, 1) }
cpus = { 16 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
memory = { 64.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
time = { 96.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
}
withLabel: process_long {
time = { 96.h * factor(task, 1) }
time = { 96.h * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
}
withLabel: 'process_high_memory|memory_max' {
memory = { 128.GB * factor(task, 1) }
memory = { 128.GB * (task.exitStatus in params.exit_status_scaling ? task.attempt : 1) }
}
withLabel: cpus_max {
cpus = { 32 * factor(task, 2) }
}
}

// Function to finely control the increase of the resource allocation
def factor(task, slow_factor = 1) {
if ( task.exitStatus in [143,137,104,134,139,247] ) {
return Math.ceil( task.attempt / slow_factor) as int
} else {
return 1 as int
cpus = { 32 * (task.exitStatus in params.exit_status_scaling ? Math.ceil(task.attempt/2) : 1) }
}
}
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