Automated SRA downloading, processing and Freyja analysis pipeline.
git clone https://github.com/dylanpilz/Freyja-SRA.git
cd Freyja-SRA
nextflow run main.nf -entry [sra|rerun_demix] -profile [docker|singularity] --accession_list [accession_list.csv] --output_dir [output_dir] --num_samples [num_samples]
-
-entry
- The pipeline entry point.-
sra
will download, process and run Freyja on the provided SRA accessions.--accession_list
- A CSV file containing a list of SRA accessions to download and process. The CSV file should have a header row and the first column should be namedaccession
.
-
rerun_demix
will run freyja demix step on previously generated variants output files in the provided variants directory. This is useful if you want to run Freyja on existing data with a different barcode set.--variants_dir
must contain files in the format[base_name].variants.tsv [base_name].depths.tsv
for each sample.
-
--output_dir
- The final output directory. Createsvariants
,demix
, andcovariants
subdirectories containing respective output files. (default:./outputs
) -
--num_samples
- The number of samples to process. (default: 200)
-
Addtional configuration options can be found in nextflow.config
Freyja-SRA is currently in the process of downloading and processing all publicly available SRA data, fetched with the following search terms:
'(Wastewater[All Fields] OR wastewater metagenome[All Fields]) AND ("Severe acute respiratory syndrome coronavirus 2"[Organism] OR SARS-CoV-2[All Fields])
In addition, to the above search terms, we exclude accessions that don't meet the following metadata requirements:
- Missing collection date
- Missing catchment size (
ww_population
) - Missing location (
geo_loc_name
)
To check the status of each accession, please refer to the sample_status
column in data/all_metadata.csv
. All currently processed freyja outputs are publicly available via Google Cloud Storage at gs://outbreak-ww-data