drs-nf

Nextflow to download omics data from DRS (Data Repository Service) based platforms.

This Nextflow pipeline contains a single process based on fasp-scripts

Read more resources related to DRS -

• https://github.com/ga4gh/ga4gh-drs-client
• https://github.com/ga4gh/data-repository-service-schemas

Usage

--reads         A CSV file with particular set of columns
--key_file      Credentials file
--genome_fasta  A genome fasta file (required for CRAM files)
--gcp_id        Google cloud project ID

Run with data from AnviL Gen3-DRS

You will be needing two things from - https://gen3.theanvil.io/

1. manifest file
2. credentials file

Original downloaded manifest.json (example) file need to be converted into manifest.csv (example) in order to be accepted in --reads, for doing that you can do this -

pip install csvkit
in2csv manifest.json > manifest.csv

NOTE: Make sure the manifest.csv file have five columns, Check from examples

Downloaded credentials.json file can be provided in --key_file param.

NOTE: Make sure credentials.json is a latest one. They have expiry dates when you download.

If you running with AnviL Gen3-DRS files you also need to provide a Genome fasta file with --genome_fasta, which will be used to convert CRAM files to BAM format.