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121 lines
3.9 KiB
Plaintext
121 lines
3.9 KiB
Plaintext
// Config profile metadata
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params {
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config_profile_description = 'The Sage Bionetworks profile'
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config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)'
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config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows'
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}
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// Leverage us-east-1 mirror of select human and mouse genomes
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params {
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igenomes_base = 's3://sage-igenomes/igenomes'
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max_memory = '128.GB'
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max_cpus = 16
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max_time = '240.h'
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}
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// Enable retries globally for certain exit codes
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process {
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errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }
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maxRetries = 5
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maxErrors = '-1'
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}
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// Increase time limit to allow file transfers to finish
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// The default is 12 hours, which results in timeouts
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threadPool.FileTransfer.maxAwait = '24 hour'
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// Configure Nextflow to be more reliable on AWS
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aws {
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region = "us-east-1"
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client {
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uploadChunkSize = 209715200
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uploadMaxThreads = 4
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}
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batch {
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maxParallelTransfers = 1
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maxTransferAttempts = 5
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delayBetweenAttempts = '120 sec'
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}
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}
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executor {
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name = 'awsbatch'
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// Ensure unlimited queue size on AWS Batch
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queueSize = 500
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// Slow down the rate at which AWS Batch jobs accumulate in
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// the queue (an attempt to prevent orphaned EBS volumes)
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submitRateLimit = '5 / 1 sec'
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}
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// Adjust default resource allocations (see `../docs/sage.md`)
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process {
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cpus = { check_max( 1 * slow(task.attempt), 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 24.h * task.attempt, 'time' ) }
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// Process-specific resource requirements
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withLabel:process_low {
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cpus = { check_max( 4 * slow(task.attempt), 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 24.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = { check_max( 12 * slow(task.attempt), 'cpus' ) }
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memory = { check_max( 36.GB * task.attempt, 'memory' ) }
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time = { check_max( 48.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = { check_max( 24 * slow(task.attempt), 'cpus' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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time = { check_max( 96.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 192.h * task.attempt, 'time' ) }
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}
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withLabel:process_high_memory {
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memory = { check_max( 128.GB * task.attempt, 'memory' ) }
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}
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}
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// Function to slow the increase of the resource multipler
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// as attempts are made. The rationale is that the number
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// of CPU cores isn't a limiting factor as often as memory.
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def slow(attempt, factor = 2) {
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return Math.ceil( attempt / factor) as int
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}
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// Function to ensure that resource requirements don't go
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// beyond a maximum limit (copied here for Sarek v2)
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def check_max(obj, type) {
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if (type == 'memory') {
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try {
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if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
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return params.max_memory as nextflow.util.MemoryUnit
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'time') {
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try {
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if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
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return params.max_time as nextflow.util.Duration
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else
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return obj
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} catch (all) {
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println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
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return obj
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}
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} else if (type == 'cpus') {
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try {
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return Math.min( obj, params.max_cpus as int )
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} catch (all) {
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println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
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return obj
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}
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}
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}
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