gnomad_qc.v5.resources.basics

Script containing generic resources.

Module Functions

gnomad_qc.v5.resources.basics.qc_temp_prefix([...])

Return path to temporary QC bucket.

gnomad_qc.v5.resources.basics.get_checkpoint_path(name)

Create a checkpoint path for Table or MatrixTable.

gnomad_qc.v5.resources.basics.get_logging_path(name)

Create a path for Hail log files.

Script containing generic resources.

gnomad_qc.v5.resources.basics.qc_temp_prefix(version='5.0', environment='dataproc')[source]

Return path to temporary QC bucket.

Parameters:

  • version (str) – Version of annotation path to return.

  • env – Compute environment, either ‘dataproc’ or ‘rwb’. Defaults to ‘dataproc’.

  • environment (str) –

Return type:

str

Returns:

Path to bucket with temporary QC data.

gnomad_qc.v5.resources.basics.get_checkpoint_path(name, version='5.0', mt=False, environment='dataproc')[source]

Create a checkpoint path for Table or MatrixTable.

Parameters:

  • name (str) – Name of intermediate Table/MatrixTable.

  • version (str) – Version of annotation path to return.

  • mt (bool) – Whether path is for a MatrixTable, default is False.

  • environment (str) – Compute environment, either ‘dataproc’ or ‘rwb’. Defaults to ‘dataproc’.

  • name –

  • mt –

Return type:

str

Returns:

Output checkpoint path.

gnomad_qc.v5.resources.basics.get_logging_path(name, version='5.0')[source]

Create a path for Hail log files.

Parameters:

  • name (str) – Name of log file.

  • version (str) – Version of annotation path to return.

Return type:

str

Returns:

Output log path.