README.md

sdp-wastewater

Calculate and extract the required metadata fields for the RADx-rad Wastewater RNA-Seq project

Dictionaries used:

• https://docs.google.com/spreadsheets/d/1G49OvMocM8BC4VvQ_XH6CBYYXN3a6sZ23t8KcGgIQfM/edit?usp=sharing
• https://docs.google.com/spreadsheets/d/1Lq5G_J4mggpmeqDGryKwBbHUDoXzF_zx/edit?usp=sharing&ouid=110084142835466802195&rtpof=true&sd=true

A. Build the Docker

docker pull rocker/tidyverse:4.2.2
docker build -t sdp-interop:1.2.0  .

B. Run the code:

docker run --rm \
-v <RUN_LOCAL_FOLDER>:/data_raw/  \
-v <CONSTANTS_LOCAL_FOLDER>:/constants_folder/ \
-v <OUTPUT_LOCAL_FOLDER>:/data_output/ \
sdp-interop:1.2.0  Rscript /constants_folder/Wastewater_Processing.R 

Parameters

• <RUN_LOCAL_FOLDER> : location of the run folder (e.g. ./220401_NB501949_0418_AHJ73VAFX3/)

• <CONSTANTS_LOCAL_FOLDER> : location of the folder containing the constants table (constants.xlsx) and the R script (Wastewater_Processing.R)

• <OUTPUT_LOCAL_FOLDER> : folder for output table (final_output.csv)