diff --git a/conf/azurebatchdev.config b/conf/azurebatchdev.config index 3266145d..6b13aa19 100644 --- a/conf/azurebatchdev.config +++ b/conf/azurebatchdev.config @@ -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 { @@ -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 @@ -59,10 +66,10 @@ 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; @@ -70,10 +77,10 @@ azure { ''' } 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; @@ -81,10 +88,10 @@ azure { ''' } 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; @@ -92,10 +99,10 @@ azure { ''' } 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; @@ -103,10 +110,10 @@ azure { ''' } 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; diff --git a/conf/pipeline/eager/maestro.config b/conf/pipeline/eager/maestro.config index fb1be0bd..4281ad14 100644 --- a/conf/pipeline/eager/maestro.config +++ b/conf/pipeline/eager/maestro.config @@ -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 " - } @@ -19,44 +18,44 @@ 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') } } } } @@ -64,43 +63,43 @@ profiles { 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') } } } } @@ -108,9 +107,9 @@ profiles { process { errorStrategy = 'finish' - cpus = 5 - memory = 200.GB - time = 8760.h - + cpus = 5 + memory = 200.GB + time = 8760.h } } +}