flusra: Documentation

You can run the pipeline with the following command:

nextflow run https://github.com/andersen-lab/flusra.git -r 'main' -c /nextflow.config -profile <mamba,conda>

Parameters in the nextflow.config file

• bioproject: The BioProject ID to fetch the data from NCBI.
• email: The email address to use for the NCBI API.
• only_fetch: If true, only fetch the metadata from NCBI and save it to the outdir directory.
• fetch_and_pull: If true, fetch the metadata from NCBI and pulls the new data from SRA.
• metadata: Provide an existing metadata file to bypass processing already processed SRA data
• reference: The reference genome to use for mapping.
• sra_accessions: The SRA accessions to process. Provide a list of SRA accessions to process without a BioProject ID skips fetching metadata.
• outdir: The output directory where the results will be saved.

If you want to run the pipeline with a different configuration, you can create a new nextflow.config file and provide the path to the -c option.

Please report any issues and suggestions regarding the pipeline to the issue tracker.