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Make pipeline configs strict syntax compatible #1017

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cf61456
make pipeline configs strict syntax compatible
nvnieuwk Feb 18, 2026
447ffb2
Merge branch 'master' into strict/pipeline-configs
jfy133 Mar 19, 2026
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2 changes: 1 addition & 1 deletion conf/pipeline/deepmodeloptim/crg.config
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ profiles {
singularity {
enabled = true
envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES"
if (params.use_gpu) { singularity.runOptions = '--nv' }
runOptions = params.get('use_gpu', false) ? '--nv' : ''
pullTimeout = "60m"
}
}
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141 changes: 73 additions & 68 deletions conf/pipeline/eager/eva.config
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90 changes: 48 additions & 42 deletions conf/pipeline/eager/maestro.config
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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: $obj"
return obj
}
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2 changes: 1 addition & 1 deletion conf/pipeline/methylseq/ku_sund_danhead.config
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Expand Up @@ -11,6 +11,6 @@ process {
stageInMode = 'copy'
}
withName: 'NFCORE_METHYLSEQ:METHYLSEQ:BISMARK:BISMARK_ALIGN' {
multicore = 1
ext.args = '--multicore 1'
}
}
2 changes: 1 addition & 1 deletion conf/pipeline/multiplesequencealign/crg.config
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Expand Up @@ -14,7 +14,7 @@ profiles {
singularity {
enabled = true
envWhitelist = "CUDA_VISIBLE_DEVICES,NVIDIA_VISIBLE_DEVICES"
if (params.use_gpu) { singularity.runOptions = '--nv' }
runOptions = params.get('use_gpu', false) ? '--nv' : ''
pullTimeout = "60m"
}
}
Expand Down
8 changes: 1 addition & 7 deletions conf/pipeline/proteinfold/nci_gadi.config
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Expand Up @@ -12,8 +12,6 @@ profiles {
// Define process resource limits
process {
executor = 'pbspro'
project = System.getenv("PROJECT")
storage = params.storage_account?.trim() ? params.storage_account : "scratch/${params.project}+gdata/${params.project}"
module = 'singularity'
cache = 'lenient'
stageInMode = 'symlink'
Expand All @@ -22,7 +20,6 @@ profiles {
withName: 'RUN_ALPHAFOLD2|RUN_ALPHAFOLD2_PRED|RUN_ALPHAFOLD2_MSA' {
queue = params.use_gpu ? 'gpuvolta' : 'normal'
cpus = 48
gpus = 4
time = '4h'
memory = 380.GB
}
Expand All @@ -31,7 +28,6 @@ profiles {
container = "nf-core/proteinfold_colabfold:1.1.1"
queue = params.use_gpu ? 'gpuvolta' : 'normal'
cpus = 48
gpus = 4
time = '4h'
memory = 380.GB
}
Expand All @@ -40,18 +36,16 @@ profiles {
container = "nf-core/proteinfold_esmfold:1.1.1"
queue = params.use_gpu ? 'gpuvolta' : 'normal'
cpus = 48
gpus = 4
time = '4h'
memory = 380.GB
}
}

// Write custom trace file with outputs required for SU calculation
def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
trace {
enabled = true
overwrite = false
file = "./gadi-nf-core-trace-${trace_timestamp}.txt"
file = "./gadi-nf-core-trace-${new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')}.txt"
fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
}
}
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26 changes: 14 additions & 12 deletions conf/pipeline/sarek/cfc.config
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@@ -1,5 +1,7 @@
// Profile config names for nf-core/configs

validation.ignoreParams = ['sarek_cfc_check_resource_func']

params {
// Specific nf-core/configs params
config_profile_contact = 'Friederike Hanssen (@FriederikeHanssen)'
Expand All @@ -9,34 +11,34 @@ params {
// Specific nf-core/sarek process configuration
process {
withName:'StrelkaSingle|Strelka|StrelkaBP|MantaSingle|Manta' {
cpus = { check_resource( 20 * task.attempt) }
memory = { check_resource( 59.GB * task.attempt) }
cpus = { params.sarek_cfc_check_resource_func( 20 * task.attempt) }
memory = { params.sarek_cfc_check_resource_func( 59.GB * task.attempt) }
}
withName:'MSIsensor_scan|MSIsensor_msi' {
memory = { check_resource( 55.GB * task.attempt ) }
memory = { params.sarek_cfc_check_resource_func( 55.GB * task.attempt ) }

}
withName:BamQC {
memory = { check_resource( 372.GB * task.attempt) }
memory = { params.sarek_cfc_check_resource_func( 372.GB * task.attempt) }
}

withName:MapReads{
cpus = { check_resource( 20 * task.attempt ) }
memory = { check_resource( 59.GB * task.attempt) }
cpus = { params.sarek_cfc_check_resource_func( 20 * task.attempt ) }
memory = { params.sarek_cfc_check_resource_func( 59.GB * task.attempt) }
}
}

def check_resource(obj) {
params.sarek_cfc_check_resource_func = { obj ->
try {
if (obj.getClass() == nextflow.util.MemoryUnit && obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else if (obj.getClass() == nextflow.util.Duration && obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
if (obj.getClass() == nextflow.util.MemoryUnit && obj.compareTo(params.max_memory as MemoryUnit) == 1)
return params.max_memory as MemoryUnit
else if (obj.getClass() == nextflow.util.Duration && obj.compareTo(params.max_time as Duration) == 1)
return params.max_time as Duration
else if (obj.getClass() == java.lang.Integer)
return Math.min(obj, params.max_cpus as int)
else
return obj
} catch (all) {
} catch (_) {
println " ### ERROR ### Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}' is not valid! Using default value: $obj"
}
}
4 changes: 0 additions & 4 deletions conf/pipeline/sarek/icr_davros.config
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Expand Up @@ -6,8 +6,4 @@
process {
errorStrategy = { task.exitStatus in [104, 134, 137, 139, 141, 143, 255] ? 'retry' : 'finish' }
maxRetries = 5
withName: MapReads {
memory = { check_resource(12.GB) }
time = { check_resource(48.h * task.attempt) }
}
}
8 changes: 4 additions & 4 deletions conf/pipeline/scflow/imperial.config
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Expand Up @@ -6,13 +6,13 @@ params {
config_profile_contact = 'NA'

// Analysis Resource Params
ctd_folder = "/rds/general/user/${USER}/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd"
ensembl_mappings = "/rds/general/user/${USER}/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/src/ensembl-ids/ensembl_mappings.tsv"
ctd_folder = "/rds/general/user/${System.getenv('USER')}/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/refs/ctd"
ensembl_mappings = "/rds/general/user/${System.getenv('USER')}/projects/ukdrmultiomicsproject/live/Analyses/scFlowResources/src/ensembl-ids/ensembl_mappings.tsv"
}

singularity {
enabled = true
autoMounts = true
cacheDir = "/rds/general/user/${USER}/projects/ukdrmultiomicsproject/live/.singularity-cache"
runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/${USER}/ephemeral/tmp/:/tmp,/rds/general/user/${USER}/ephemeral/tmp/:/var/tmp"
cacheDir = "/rds/general/user/${System.getenv('USER')}/projects/ukdrmultiomicsproject/live/.singularity-cache"
runOptions = "-B /rds/,/rdsgpfs/,/rds/general/user/${System.getenv('USER')}/ephemeral/tmp/:/tmp,/rds/general/user/${System.getenv('USER')}/ephemeral/tmp/:/var/tmp"
}
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