Modify Sample Name or Barcode Group in AbXtract Dataset

This cube will allow for straightforward addition of fields associated with sample_name, barcode_group and barcode_roundif it was not added during the barcoding step

Parameter Details

Calculation Parameters

  • Barcode Group (barcode_group) type: string: Input a barcode group, if desired (shorter is better). No commas or colons. Any commas(,) or colons(:) replaced with ‘_’ NOTE:

  1. Will overwrite existing values.

  2. If nothing input, will keep same value as before

  3. IMPORTANT: if barcode_group is assigned, it will update the seq_id to reflect this change with new barcode_group
    Default: “”
    • Barcode Round (barcode_round) type: string: Input a barcode round, must be ‘early’ or ‘late’ or ‘None’, NOTE:

  1. Will overwrite existing values.

  2. If nothing input, will keep same value as before
    Default: None
    Choices: early, late, None
    • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
      Default: 1 , Min: 1, Max: 128
    • Cube Metrics (cube_metrics) type: string: Set of metrics to be collected

      Choices: cpu, disk, memory, network
    • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
      Default: 5120.0 , Min: 128.0, Max: 8589934592
    • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
      Default: 0 , Max: 16
    • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
      Default: “”
    • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
    • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
      Default: 1800 , Min: 256.0, Max: 8589934592
    • Metric Period (metric_period) type: decimal: How often to sample metrics, in seconds
      Default: 60
      Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
    • Sample Name Input (sample_name) type: string: Input a sample name (if desired), (shorter is better). No commas or colons. Any commas(,) or colons(:) replaced with ‘_’ NOTE:

  1. Will overwrite existing values.

  2. If nothing input, will keep same value as before
    Default: “”
    • Sequence Type (sequence_type) type: string: Indicates whether sequence is sanger or ngs
      Default: NGS
      Choices: Sanger, NGS
    • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
      Default: 64
    • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
      Default: Prohibited
      Choices: Allowed, Preferred, NotPreferred, Prohibited, Required

Hardware Parameters

Machine hardware requirements
  • Memory (MiB) (memory_mb) type: decimal: The minimum amount of memory in MiBs (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 1800 , Min: 256.0, Max: 8589934592
  • Shared Memory (MiB) (shared_memory_mb) type: decimal: The amount of shared memory to allow a container to address
    Default: 64
  • Temporary Disk Space (MiB) (disk_space) type: decimal: The minimum amount of disk space in MiB (1048576 B) this cube requires. Due to overhead, request a couple hundred MiB more than required.
    Default: 5120.0 , Min: 128.0, Max: 8589934592
  • GPUs (gpu_count) type: integer: The number of GPUs to run this cube with
    Default: 0 , Max: 16
  • CPUs (cpu_count) type: integer: The number of CPUs to run this cube with
    Default: 1 , Min: 1, Max: 128
  • Instance Type (instance_type) type: string: The type of instance that this cube needs to be run on
  • Spot policy (spot_policy) type: string: Control cube placement on spot market instances
    Default: Prohibited
    Choices: Allowed, Preferred, NotPreferred, Prohibited, Required
  • Instance Tags (instance_tags) type: string: Only run on machines with matching tags (comma separated)
    Default: “”

Metrics Parameters

Cube Metric Parameters
  • Metric Period (None) type: decimal: How often to sample metrics, in seconds
    Default: 60
    Choices: 1, 5, 10, 30, 60, 120, 180, 240, 300, Min: 1, Max: 300
  • Cube Metrics (None) type: string: Set of metrics to be collected

    Choices: cpu, disk, memory, network