Run bwtool summary

[marcelm]

The shell script that does the scaling/normalization runs bwtool summary. This is not implemented in the Snakemake pipeline, yet.

[marcelm]

@simonelsasser mentioned that one can also use deepTools, R or Python to extract summary statistics instead.

[marcelm]

The bwtool summary command is run on a couple of BED files, such as ChromHMM17.bed and K27_genes_bwtool.bed. If we integrate this or a similar tool into the pipeline, we would need a way to configure which BED files to run it on. Ideas:

• List the paths to the BED files in the configuration file
• Use all BED files that exist in a subdirectory; then the user would have to create symlinks in it

[cnluzon]

I'm more inclined to use the BED paths in the config, even though it can be a bit tiresome to specify each one, I think it pays off in flexibility. And if it turns out the BED files we use don't usually change, configure once and run many times.

[marcelm]

Yes, good point. This also brings up the point of how to run the pipeline on many datasets easily, need to think about that.