This compiles my notes for conda and snakemake.
update conda environment from yaml
source activate myenv conda env update --file environment.yaml
Snakemake is a fantastic tool to keep the running environment constant, document data processing and reproduce the analysis when necessary. I think it currently lacks the functionality of recording down the thought process behind each data processing decision, but perhaps that can be left as comments in the file and finally documented somewhere else.
use directory as output
use mutliple files as input
Refer to here. Basically one needs to extend both the input and output file names for the function to work.
Sometimes no-rule error can be caused because a similar rule has been executed. Use
-R rule_name to resolve this issue.