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Merge pull request #297 from vsmalladi/azure
Add in template for Azure Workflow
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commit
291fcb20a5
5 changed files with 63 additions and 1 deletions
1
.github/workflows/main.yml
vendored
1
.github/workflows/main.yml
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@ -21,6 +21,7 @@ jobs:
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- 'alice'
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- 'aws_tower'
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- 'awsbatch'
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- 'azurebatch'
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- 'bi'
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- 'bigpurple'
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- 'binac'
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@ -88,6 +88,7 @@ Currently documentation is available for the following systems:
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* [ALICE](docs/alice.md)
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* [AWSBATCH](docs/awsbatch.md)
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* [AWS_TOWER](docs/aws_tower.md)
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* [AZUREBATCH](docs/azurebatch.md)
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* [BIGPURPLE](docs/bigpurple.md)
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* [BI](docs/bi.md)
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* [BINAC](docs/binac.md)
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25
conf/azurebatch.config
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25
conf/azurebatch.config
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//Nextflow config file for running on Azure batch
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params {
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config_profile_description = 'AWSBATCH Cloud Profile'
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config_profile_contact = 'Venkat Malladi (@vsmalladi)'
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config_profile_url = 'https://azure.microsoft.com/services/batch/'
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az_location = 'westus2'
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batch_name = false
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batch_key = false
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storage_name = false
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sas_token = false
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}
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docker {
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enabled = true
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}
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azure.batch.location = params.az_location
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azure.batch.accountName = params.batch_name
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azure.batch.accountKey = params.batch_key
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azure.batch.autoPoolMode = true
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azure.storage.accountName = params.storage_name
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azure.storage.sasToken = params.sas_token
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process.executor = 'azurebatch'
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34
docs/azurebatch.md
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34
docs/azurebatch.md
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@ -0,0 +1,34 @@
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# nf-core/configs: azurebatch Configuration
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To be used with the `azurebatch` profile by specifying the `-profile azurebatch` when running nf-core pipelines.
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Custom queue and storage need to be supplied with `params.az_location`, `params.batch_name`, `params.batch_key`, `params.storage_name`, `params.sas_token`.
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## Required Parameters
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### `--az_location`
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The Azure Batch region where the computation is executed in VMs. Default (`westus2`).
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### `--batch_name`
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The Azure Batch account name.
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### `--batch_key`
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The Azure Batch account key.
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### `--storage_name`
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The Azure Blob Storage name. Example is currently [Illumina Platinum Genomes](https://docs.microsoft.com/en-us/azure/open-datasets/dataset-illumina-platinum-genomes?tabs=azure-storage). **This must be changed to your specific storage account.**
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### `--sas_token`
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The Azure Blob Storage shared access signature token. Example is currently [Illumina Platinum Genomes](https://docs.microsoft.com/en-us/azure/open-datasets/dataset-illumina-platinum-genomes?tabs=azure-storage). **This must be changed to your specific storage account.**
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### `-w`
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The Azure Blob container to be used as Nextflow work directory (`-w az://work`).
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## Azure Batch Setup
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Please refer to the [Nextflow](https://www.nextflow.io/docs/edge/azure.html) documentation which describe how to setup the Azure Batch environment.
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@ -14,6 +14,7 @@ profiles {
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alice { includeConfig "${params.custom_config_base}/conf/alice.config" }
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aws_tower { includeConfig "${params.custom_config_base}/conf/aws_tower.config" }
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awsbatch { includeConfig "${params.custom_config_base}/conf/awsbatch.config" }
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azurebatch { includeConfig "${params.custom_config_base}/conf/azurebatch.config" }
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bi { includeConfig "${params.custom_config_base}/conf/bi.config" }
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bigpurple { includeConfig "${params.custom_config_base}/conf/bigpurple.config" }
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binac { includeConfig "${params.custom_config_base}/conf/binac.config" }
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@ -40,7 +41,7 @@ profiles {
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icr_davros { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
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ifb_core { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
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imperial { includeConfig "${params.custom_config_base}/conf/imperial.config" }
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imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
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imperial_mb { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }
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jax { includeConfig "${params.custom_config_base}/conf/jax.config" }
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lugh { includeConfig "${params.custom_config_base}/conf/lugh.config" }
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maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" }
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