#hi Yall this is a semi edited version of the pipeline, some of this is relevant, but the sickle part might need to be changed. #if you want similar read trimming then it probably doesn't matter

MultiOMIC analysis of cfRNA sequencing pipeline

Rowan Callahan and Elias Spiliotopolous

The following pipeline has around four different parts:

1: Snakemake

• This will have our main snakefile and our five different sub rules that we use

2: Environments

• all of the config yaml files that we use w conda to setup environments
• You will need to include on eenvironment called omic qc which should only need

3: Output Folders

• data for all of the intermediary results
• results for all of our tabulated results

4: Config files

• config.yaml here
• config.yaml in the profile

Before Running, you will need too:

1: Link samples into a samples/raw directory in the base folder

2: Change the Gscratch location at the bottom of the config.yaml file

3: Add a tab-delimited txt file containing the metadata for the samples

TODO:

1: get samples names from the metadata not from the file locations need to adapt the file linking script that we are currently using 2: Start minimum viable submittable job for pipeline overall 3: finish readme and config setup for the pipeline 4: setup for new pipeline usage script