NWSS Sequence Submission User Guide¶
Overview¶
This workflow uses Nextflow to automate submission of FASTQ read files to NCBI's SRA database. It includes three steps. + Metadata validation: Check that your Excel data conforms to NCBI expectations + Biosample submission: Submit each sample to Biosample database and return Biosample ID + SRA submission: Submit each FASTQ file to SRA database and return an Accession ID
We recommend that you use the singularity or docker profile if possible, and only use conda when containers are not an option.
1. Prerequisites¶
- Review Nextflow Getting Started if you have never used Nextflow before
- Install Nextflow
- Clone the TOSTADAS GitHub repository:
git clone https://github.com/CDCgov/tostadas.git - Register for an NCBI Center Account
- Create an NCBI Bioproject. Link to the NWSS umbrella Bioproject (PRJNA747181).
2. Fill out Metadata for all samples¶
Download the Excel template for wastewater metadata and fill out following the examples in the sheet. Rename your file.
3. Fill out the submission config file¶
Add your center information to this configuration file. Make sure for Biosample package you enter SARS-CoV-2: wastewater surveillance; version 1.0. Rename the file as needed, but make sure you keep it in the conf/ directory.
4. Test your set up with the test profile¶
Run the following command to test your setup nextflow run main.nf -profile nwss,test,[docker,singularity,conda]
5. Run a test with real data¶
Add a few of your actual samples to the Excel metadata sheet and submit these to the test server. NCBI provides a test server to validate the sftp connection before submitting to production.
nextflow run main.nf -profile nwss,<docker|singularity|conda> --meta_path <path/to/metadata_file.xlsx> --submission_config <path/to/submission_config.yaml> --outdir <path/to/outdir>
6. Submit small sample to production server¶
nextflow run main.nf -profile nwss,<docker|singularity|conda> --meta_path <path/to/metadata_file.xlsx> --submission_config <path/to/submission_config.yaml> --outdir <path/to/outdir> --prod_submission true
7. Submit all samples to production server¶
Update your metadata path to point to all of your samples for submissions nextflow run main.nf -profile nwss,<docker|singularity|conda> --meta_path <path/to/metadata_file.xlsx> --submission_config <path/to/submission_config.yaml> --outdir <path/to/outdir> --prod_submission true
8. Troubleshooting¶
View the docs