You can run pipeline on GTEX data otained directly from Gen3-DRS if you specify input option:
--download_from 'GTEX'
You will be needing two things from - https://gen3.theanvil.io/
- manifest file
- credentials file
Original downloaded manifest.json will be converted into manifest.csv with pipeline using: https://csvkit.readthedocs.io/en/latest/
The manifest.csv will be subset using the reads.csv file provided in --reads param. (This allows you to download a complete manifest and later select the samples of interest.) For example: gtex.reads
Downloaded credentials.json file can be provided in --key_file param.
NOTE: Make sure credentials.json is a latest one. They have expiration dates when you download.
If you running with AnviL Gen3-DRS to download CRAM files you also need to provide a Genome fasta file with --genome_fasta, which will be used to convert CRAM files to BAM format. If you are donwloading bam files, you can skip this parameter.
For a minimal params list check gtex.config