I am trying to make directories for the different "IDs" I have stored in the .csv file (they are stored under column "ID"). However, snakemake doesn't seem to be able to detect "IDs" in output from run.
rule make_directories: input:"exptXXXXX_metadata.csv" output: directory(expand("tissues/{id}", id = IDs)) run: import pandas as pd df = pd.read_csv('exptXXXXX_metadata.csv') ##unique IDs which I want to make different directories of under the parent_dir "tissues" IDs = set(df['ID']) for i in IDs: f = output[id] shell("mkdir {f}")I have tried different suggestions from the snakemake documentation: https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-do-i-access-elements-of-input-or-output-by-a-variable-index