module plugins.sample_fetchers.sra

Fetch remote samples from SRA.

Global Variables

• columns_sra_in
• map_model_to_sra_in
• map_sra_out_to_model

---

class SampleFetcherSRA

Fetch remote samples from SRA.

Args:

• records: Pandas DataFrame object.
• config: Config object.

Attributes:

• records: Pandas DataFrame object.
• config: Config object.

---

method process

process(
    loc: Path = PosixPath('/home/runner/work/zarp-cli/zarp-cli'),
    workflow: Path = PosixPath('Snakefile')
) → DataFrame

Fetch remote samples from SRA.

Args:

• loc: Path to fetch samples to. Samples may be located within child directories. Defaults to current working directory.
• workflow: Path to Snakemake workflow for fetching samples from SRA. Defaults to Snakefile in current working directory.

Returns: Dataframe with local path information for sequencing libraries.