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FIX: Strict syntax for eager/maestro #1084

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FIX: Strict syntax for eager/maestro #1084

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bf7d4a3
FIX: Strict syntax for eager/maestro
maxulysse Apr 7, 2026
9c310c2
Merge branch 'master' into eager/maestro
maxulysse Apr 14, 2026
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90 changes: 48 additions & 42 deletions conf/pipeline/eager/maestro.config
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,12 @@
* nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear, mitocondrial or unlimitedtime)
*/

validation {
ignoreParams = [
'eager_maestro_check_max_func'
]
}

params {

config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
Expand All @@ -21,41 +27,41 @@ profiles {
maxRetries = 2

withName: makeBWAIndex {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(12.h * task.attempt, 'time') }
cpus = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
}
withName: adapter_removal {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(12.h * task.attempt, 'time') }
cpus = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(16.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
}
withName: bwa {
cpus = { check_max(40 * task.attempt, 'cpus') }
memory = { check_max(40.GB * task.attempt, 'memory') }
cpus = { params.eager_maestro_check_max_func(40 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(40.GB * task.attempt, 'memory') }
time = 24.h
cache = 'deep'
}
withName: markduplicates {
errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
cpus = { check_max(16 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(12.h * task.attempt, 'time') }
cpus = { params.eager_maestro_check_max_func(16 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(16.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
}
withName: damageprofiler {
cpus = 1
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
}
withName: fastp {
cpus = 8
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
}
withName: fastqc {
cpus = 2
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
}
}
}
Expand All @@ -66,40 +72,40 @@ profiles {
maxRetries = 2

withName: makeBWAIndex {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(12.h * task.attempt, 'time') }
cpus = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
}
withName: adapter_removal {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(12.h * task.attempt, 'time') }
cpus = { params.eager_maestro_check_max_func(8 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(16.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(12.h * task.attempt, 'time') }
}
withName: bwa {
cpus = { check_max(5 * task.attempt, 'cpus') }
memory = { check_max(5.GB * task.attempt, 'memory') }
cpus = { params.eager_maestro_check_max_func(5 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
time = 24.h
}
withName: markduplicates {
errorStrategy = { task.exitStatus in [143, 137, 104, 134, 139] ? 'retry' : 'finish' }
cpus = { check_max(5 * task.attempt, 'cpus') }
memory = { check_max(5.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
cpus = { params.eager_maestro_check_max_func(5 * task.attempt, 'cpus') }
memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
}
withName: damageprofiler {
cpus = 1
memory = { check_max(5.GB * task.attempt, 'memory') }
time = { check_max(3.h * task.attempt, 'time') }
memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(3.h * task.attempt, 'time') }
}
withName: fastp {
cpus = 8
memory = { check_max(5.GB * task.attempt, 'memory') }
time = { check_max(3.h * task.attempt, 'time') }
memory = { params.eager_maestro_check_max_func(5.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(3.h * task.attempt, 'time') }
}
withName: fastqc {
cpus = 2
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
memory = { params.eager_maestro_check_max_func(8.GB * task.attempt, 'memory') }
time = { params.eager_maestro_check_max_func(6.h * task.attempt, 'time') }
}
}
}
Expand All @@ -117,31 +123,31 @@ profiles {
// Function to ensure that resource requirements don't go beyond
// a maximum limit
// FOR DSL1 PIPELINE ONLY!
def check_max(obj, type) {
params.eager_maestro_check_max_func = { obj, type ->
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
if (obj.compareTo(params.max_memory as MemoryUnit) == 1)
return params.max_memory as MemoryUnit
else
return obj
} catch (all) {
} catch (_) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
if (obj.compareTo(params.max_time as Duration) == 1)
return params.max_time as Duration
else
return obj
} catch (all) {
} catch (_) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
} catch (_) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
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