Move all of the version dependency files from GitHub to ref_folder. Idea: the version of reference only depends on the version of the reference folder you download. It won't be affected by the files from the GitHub repository.
tx2gene file is the file to convert the gene transcript to gene symbol. Since this is the version dependency file, I move this file from the static folder to the reference folder. This file will also affect preprocessing cohort module and differential module. So I also modified the corresponding snakemake files.
remove the ./tmp folder pyPrada generated that may cause an issue when people do a second run.
change the ref.yaml to follow the new format of reference folder, and remove some unnecessary reference files.
remove some redundant "/" symbols in snakemake execution file
There are few major changes:
Move all of the version dependency files from GitHub to ref_folder. Idea: the version of reference only depends on the version of the reference folder you download. It won't be affected by the files from the GitHub repository.
tx2gene file is the file to convert the gene transcript to gene symbol. Since this is the version dependency file, I move this file from the static folder to the reference folder. This file will also affect preprocessing cohort module and differential module. So I also modified the corresponding snakemake files.
remove the ./tmp folder pyPrada generated that may cause an issue when people do a second run.
change the ref.yaml to follow the new format of reference folder, and remove some unnecessary reference files.
remove some redundant "/" symbols in snakemake execution file