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nextflow.config
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nextflow.config
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process {
container = 'quay.io/nextflow/bash'
containerOptions = ' --net=host --rm -u $(id -u):$(id -g)'
executor = 'local'
}
docker {
enabled = true
}
plugins {
id 'nf-azure'
id 'nf-amazon'
}
profiles {
local {
params {
resultsDir = 'results'
}
process{
executor = 'local'
}
}
cluster {
process {
executor = 'sge'
clusterOptions = '-S /bin/bash '
}
}
azurebatch {
process {
executor = 'azurebatch'
container = 'quay.io/nextflow/bash'
}
workDir = 'az://workdir/work' //workdir is a blob storage within the storage account
params {
resultsDir = 'az://results' //results is a blob storage within the storage account
}
azure {
batch {
location = 'eastus2'
accountName = ''
endpoint = ''
accountKey = ''
allowPoolCreation = true
autoPoolMode = true
deletePoolsOnCompletion = true
copyToolInstallMode = 'task'
pools {
auto {
vmType = 'Standard_D4_v3'
vmCount = 1
}
}
}
storage {
accountName = ''
accountKey = ''
}
registry {
server = 'docker.io'
userName = ''
password = ''
}
}
}
awsbatch {
params {
resultsDir = 's3://eipm-nextflow-results/pipeline-results/'
}
process {
executor = 'awsbatch'
container = 'quay.io/nextflow/bash'
queue='eipm-nextflow-queue'
}
aws {
// NOTE: this setting is only required if the AWS CLI tool is installed in a custom AMI
batch {
cliPath = '/home/ec2-user/miniconda/bin/aws'
}
region = 'us-east-1'
}
}
}