https://github.com/andersen-lab/flusra
https://github.com/andersen-lab/flusra
flu
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/andersen-lab/flusra
- Owner: andersen-lab
- Created: 2024-05-15T05:44:23.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-05-15T01:20:57.000Z (about 1 year ago)
- Last Synced: 2025-07-28T06:31:19.687Z (11 months ago)
- Topics: flu
- Language: Nextflow
- Homepage:
- Size: 1.25 MB
- Stars: 3
- Watchers: 1
- Forks: 4
- Open Issues: 2
-
Metadata Files:
- Readme: docs/README.md
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README
# flusra: Documentation
You can run the pipeline with the following command:
```bash
nextflow run https://github.com/andersen-lab/flusra.git -r 'main' -c /nextflow.config -profile
```
## 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](https://github.com/andersen-lab/flusra/issues).