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Minor formatting fixes #756

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merged 2 commits into from
Sep 24, 2024
Merged

Minor formatting fixes #756

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864346b
Minor formatting fixes
jfy133 Sep 23, 2024
7655403
Merge branch 'nf-core:master' into master
jfy133 Sep 23, 2024
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93 changes: 50 additions & 43 deletions conf/azurebatchdev.config
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Original file line number Diff line number Diff line change
@@ -1,32 +1,31 @@
// Nextflow config file for running on Azure batch
params {
config_profile_description = 'Azure BATCH Dev Cloud Profile'
config_profile_contact = 'Venkat Malladi (@vsmalladi)'; Abhinav Sharma (@abhi18av)'
config_profile_url = 'https://azure.microsoft.com/services/batch/'
config_profile_contact = "Venkat Malladi (@vsmalladi)'; Abhinav Sharma (@abhi18av)"
config_profile_url = 'https://azure.microsoft.com/services/batch/'

// Active Directory
principal_id = null
principal_secret = null
tenant_id = null
principal_id = null
principal_secret = null
tenant_id = null

// Storage
storage_name = null
storage_name = null

// Batch
az_location = "westus2"
batch_name = null
az_location = "westus2"
batch_name = null

vm_type = "Standard_D8s_v3"
autopoolmode = false
allowpoolcreation = true
deletejobs = true
deletepools = false
vm_type = "Standard_D8s_v3"
autopoolmode = false
allowpoolcreation = true
deletejobs = true
deletepools = false

// ACR
acr_registry = null
acr_username = null
acr_password = null

acr_registry = null
acr_username = null
acr_password = null
}

process {
Expand All @@ -36,15 +35,23 @@ process {
azure {
process {
queue = 'Standard_D2d_v4'
withLabel:process_low {queue = 'Standard_D4d_v4'}
withLabel:process_medium {queue = 'Standard_D16d_v4'}
withLabel:process_high {queue = 'Standard_D32d_v4'}
withLabel:process_high_memory {queue = 'Standard_D48d_v4'}
withLabel: process_low {
queue = 'Standard_D4d_v4'
}
withLabel: process_medium {
queue = 'Standard_D16d_v4'
}
withLabel: process_high {
queue = 'Standard_D32d_v4'
}
withLabel: process_high_memory {
queue = 'Standard_D48d_v4'
}
}
activeDirectory {
servicePrincipalId = params.principal_id
servicePrincipalId = params.principal_id
servicePrincipalSecret = params.principal_secret
tenantId = params.tenant_id
tenantId = params.tenant_id
}
storage {
accountName = params.storage_name
Expand All @@ -59,54 +66,54 @@ azure {
deletePoolsOnCompletion = params.deletepools
pools {
Standard_D2d_v4 {
autoScale = true
vmType = 'Standard_D2d_v4'
vmCount = 2
maxVmCount = 20
autoScale = true
vmType = 'Standard_D2d_v4'
vmCount = 2
maxVmCount = 20
scaleFormula = '''
$TargetLowPriorityNodes = 1;
$TargetDedicatedNodes = 0;
$NodeDeallocationOption = taskcompletion;
'''
}
Standard_D4d_v4 {
autoScale = true
vmType = 'Standard_D4d_v4'
vmCount = 2
maxVmCount = 20
autoScale = true
vmType = 'Standard_D4d_v4'
vmCount = 2
maxVmCount = 20
scaleFormula = '''
$TargetLowPriorityNodes = 1;
$TargetDedicatedNodes = 0;
$NodeDeallocationOption = taskcompletion;
'''
}
Standard_D16d_v4 {
autoScale = true
vmType = 'Standard_D16d_v4'
vmCount = 2
maxVmCount = 20
autoScale = true
vmType = 'Standard_D16d_v4'
vmCount = 2
maxVmCount = 20
scaleFormula = '''
$TargetLowPriorityNodes = 1;
$TargetDedicatedNodes = 0;
$NodeDeallocationOption = taskcompletion;
'''
}
Standard_D32d_v4 {
autoScale = true
vmType = 'Standard_D32d_v4'
vmCount = 2
maxVmCount = 20
autoScale = true
vmType = 'Standard_D32d_v4'
vmCount = 2
maxVmCount = 20
scaleFormula = '''
$TargetLowPriorityNodes = 1;
$TargetDedicatedNodes = 0;
$NodeDeallocationOption = taskcompletion;
'''
}
Standard_D48d_v4 {
autoScale = true
vmType = 'Standard_D48d_v4'
vmCount = 2
maxVmCount = 10
autoScale = true
vmType = 'Standard_D48d_v4'
vmCount = 2
maxVmCount = 10
scaleFormula = '''
$TargetLowPriorityNodes = 1;
$TargetDedicatedNodes = 0;
Expand Down
133 changes: 66 additions & 67 deletions conf/pipeline/eager/maestro.config
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,9 @@

params {

config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'

config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available "

}


Expand All @@ -19,98 +18,98 @@ profiles {
nuclear {
process {
errorStrategy = 'retry'
maxRetries = 2
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' ) }
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') }
}
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' ) }
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') }
}
withName:'bwa'{
cpus = { check_max( 40 * task.attempt, 'cpus' ) }
memory = { check_max( 40.GB * task.attempt, 'memory' ) }
time = 24.h
cache = 'deep'
withName: bwa {
cpus = { check_max(40 * task.attempt, 'cpus') }
memory = { check_max(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' ) }
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') }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
withName: damageprofiler {
cpus = 1
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(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' ) }
withName: fastp {
cpus = 8
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(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' ) }
withName: fastqc {
cpus = 2
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
}
}
}

mitocondrial {
process {
errorStrategy = 'retry'
maxRetries = 2
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' ) }
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') }
}
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' ) }
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') }
}
withName:'bwa'{
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = 24.h
withName: bwa {
cpus = { check_max(5 * task.attempt, 'cpus') }
memory = { check_max(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' ) }
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') }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
withName: damageprofiler {
cpus = 1
memory = { check_max(5.GB * task.attempt, 'memory') }
time = { check_max(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' ) }
withName: fastp {
cpus = 8
memory = { check_max(5.GB * task.attempt, 'memory') }
time = { check_max(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' ) }
withName: fastqc {
cpus = 2
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(6.h * task.attempt, 'time') }
}
}
}
unlimitedtime {
process {
errorStrategy = 'finish'

cpus = 5
memory = 200.GB
time = 8760.h

cpus = 5
memory = 200.GB
time = 8760.h
}
}
}
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