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module config.samples

ZARP sample processing.

DEPRECATED: This module is deprecated and will be removed in a future release.

A replacement will be provided in subpackage :mod:zarp.plugins.sample_dereferencers and will implement the abstract class :class:zarp.abstract_classes.sample_processors.SampleProcessor.

class SampleProcessor

Process ZARP samples.

Resolve sample references, set sample configuration, download remote samples, validate samples and produce a ZARP sample table.

Args:

  • *args: References to individual sequencing libraries by local file path or read archive identifiers OR paths to ZARP sample tables; see documentation for details.
  • sample_config: Sample configuration parameters.
  • run_config: Run configuration parameters.

Attributes:

  • references: References to individual sequencing libraries by local file path or read archive identifiers OR paths to ZARP sample tables; see documentation for details.
  • sample_config: Sample configuration parameters.
  • run_config: Run configuration parameters.
  • samples: List of sample objects.
  • samples_remote: List of remote sample objects.

method __init__

__init__(*args: str, sample_config: ConfigSample, run_config: ConfigRun) → None

Class constructor.

method set_samples

set_samples() → None

Resolve sample references and set sample configuration.

method write_remote_sample_table

write_remote_sample_table(samples: List[Sample], outpath: Path) → Path

Write table of remote samples to file.

Args:

  • samples: List of sample objects.
  • outpath: Path to write sample table to.

Returns: Path to sample table.

method write_sample_table

write_sample_table(samples: List[Sample], outpath: Path) → Path

Write table of samples to file.

Args:

  • samples: List of sample objects.
  • outpath: Path to write sample table to.

Returns: Path to sample table.