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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,67 @@ | ||
| //Nextflow config file for running on Azure batch | ||
| params { | ||
| config_profile_description = 'Azure BATCH Cloud Profile' | ||
| config_profile_contact = 'Venkat Malladi (@vsmalladi)' | ||
| config_profile_contact = 'Venkat Malladi (@vsmalladi) & Adam Talbot (@adamrtalbot)' | ||
| config_profile_url = 'https://azure.microsoft.com/services/batch/' | ||
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| az_location = 'westus2' | ||
| batch_name = false | ||
| batch_key = false | ||
| storage_name = false | ||
| sas_token = false | ||
| } | ||
| // Storage | ||
| storage_name = null | ||
| storage_key = null | ||
| storage_sas = null | ||
|
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| // Batch | ||
| az_location = "westus2" | ||
| batch_name = null | ||
| batch_key = null | ||
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| vm_type = "Standard_D8s_v3" | ||
| autopoolmode = true | ||
| allowpoolcreation = true | ||
| deletejobs = true | ||
| deletepools = true | ||
| az_worker_pool = "auto" | ||
|
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| // ACR | ||
| acr_registry = null | ||
| acr_username = null | ||
| acr_password = null | ||
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| docker { | ||
| enabled = true | ||
| } | ||
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| process { | ||
| executor = "azurebatch" | ||
| } | ||
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| azure.batch.location = params.az_location | ||
| azure.batch.accountName = params.batch_name | ||
| azure.batch.accountKey = params.batch_key | ||
| azure.batch.autoPoolMode = true | ||
| azure.storage.accountName = params.storage_name | ||
| azure.storage.sasToken = params.sas_token | ||
| process.executor = 'azurebatch' | ||
| azure { | ||
| process { | ||
| queue = params.az_worker_pool | ||
| } | ||
| storage { | ||
| accountName = params.storage_name | ||
| accountKey = params.storage_key | ||
| sasToken = params.storage_sas | ||
| } | ||
| batch { | ||
| location = params.az_location | ||
| accountName = params.batch_name | ||
| accountKey = params.batch_key | ||
| tokenDuration = "24h" | ||
| autoPoolMode = params.autopoolmode | ||
| allowPoolCreation = params.allowpoolcreation | ||
| deleteJobsOnCompletion = params.deletejobs | ||
| deletePoolsOnCompletion = params.deletepools | ||
| pools { | ||
| auto { | ||
| vmType = params.vm_type | ||
| autoScale = true | ||
| vmCount = 1 | ||
| maxVmCount = 12 | ||
| } | ||
| } | ||
| } | ||
| registry { | ||
| server = params.acr_registry | ||
| userName = params.acr_username | ||
| password = params.acr_password | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| params { | ||
| config_profile_description = 'USDA ARS SCINet Ceres Cluster profile' | ||
| config_profile_contact = 'Thomas A. Christensen II (@MillironX)' | ||
| config_profile_url = 'https://scinet.usda.gov/guide/ceres/' | ||
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| max_memory = 640.GB | ||
| max_cpus = 36 | ||
| max_time = 60.d | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| } | ||
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| process { | ||
| executor = 'slurm' | ||
| scratch = true | ||
| queue = { | ||
| switch (task.memory) { | ||
| case { it >= 216.GB }: | ||
| switch (task.time) { | ||
| case { it >= 7.d }: | ||
| return 'longmem' | ||
| default: | ||
| return 'mem' | ||
| } | ||
| default: | ||
| switch (task.time) { | ||
| case { it >= 21.d }: | ||
| return 'long60' | ||
| case { it >= 7.d }: | ||
| return 'long' | ||
| case { it >= 48.h }: | ||
| return 'medium' | ||
| default: | ||
| return 'short' | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| //Profile config names for nf-core/configs | ||
| params { | ||
| config_profile_description = 'Centre for Genomic Regulation (CRG) cluster profile provided by nf-core/configs' | ||
| config_profile_contact = 'Athanasios Baltzis (@athbaltzis)' | ||
| config_profile_url = 'http://www.linux.crg.es/index.php/Main_Page' | ||
| } | ||
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| process { | ||
| executor = 'crg' | ||
| } | ||
|
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| singularity { | ||
| enabled = true | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
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| params { | ||
| config_profile_contact = 'Kübra Narcı [email protected]' | ||
| config_profile_name = 'DKFZ cluster' | ||
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| max_cpus = 30 | ||
| max_memory = '250.GB' | ||
| max_time = '48.h' | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| } | ||
|
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| process { | ||
| executor = 'lsf' | ||
| scratch = '$SCRATCHDIR/$LSB_JOBID' | ||
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| } | ||
| executor { | ||
| name = 'lsf' | ||
| perTaskReserve = false | ||
| perJobMemLimit = true | ||
| queueSize = 10 | ||
| submitRateLimit = '3 sec' | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| // Nextflow config for running on the MIT Engaging HPC cluster | ||
| params { | ||
| config_profile_description = 'MIT Engaging HPC cluster profile.' | ||
| config_profile_contact = 'Phil Palmer (@PhilPalmer)' | ||
| config_profile_url = "https://engaging-web.mit.edu/eofe-wiki/" | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| } | ||
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| process { | ||
| executor = 'slurm' | ||
| clusterOptions = '-p sched_mit_hill' | ||
| } | ||
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| params { | ||
| max_memory = 64.GB | ||
| max_cpus = 16 | ||
| max_time = 12.h | ||
| } |
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