What is the most convenient option for running a nextflow workflow against all fastq files in an SRA project?
The workflow will run in AWS so it seems obvious to use the S3 storage of SRA, has anyone tried this before?
If you’re building a Nextflow pipeline from scratch, or want to change one, I’d recommend having a look at the fromSRA channel factory (check here for a reference). If you just want to run an already-developed pipeline that you don’t want to change, I’d recommend using SRA Toolkit to download the SRA project FASTQ files.
More info about retrieving FASTQ files from SRA projects here and here. Also check Download SRA sequence data using Amazon Web Services (AWS).