Requirements:
synapseclient: You can install synapseclient from: https://python-docs.synapse.org/build/html/index.html
synapseclient credentials: To upload files to the synapse portal you need to create an account on synpase. Otherwise you can choose a different place to upload files like AWS S3. To upload files to AWS S3 you will need an AWS account and set up aws-cli
snakemake: You can install snakemake from: https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
snakemake file command paths: Assign the path to the FastQC command
main steps of the code is:
- Example: python run.py -studyName STUDYNAME -metaFile METAFILE.txt -synId SYNID Here SYNID is the ID of the folder on the synapse portal where the fastq files are stored.