BasicUsage

To run pipeline successfully, two files are necessary.

One is .py file which includes analysis steps, while config file which allocate necessary files. Both of them can be found in /script/

There’re two types of config files which called configForMainTail.yaml and configForModifAS.yaml.

First is used for dRNAmain and dRNAtail, while other is for dRNAmodif_1/_2 and dRNAas.py.

You needn’t to worry since the location of yaml has been assigned in .py files.

We also offer examples of config files in /examples/

 snakemake -s {dRNAmain.py / dRNAtail.py / dRNAmodif.py / dRNAas.py}
           -s the snakemake file you want to run
           --cores / -c : the number of cores to use (necessary)
           --set-threads myrule=XXX set threads XXX for running

Snakemake offer a test module, you can process dry-run to test whether there’re any error.

snakemake -s {dRNAmain.py / dRNAtail.py / dRNAmodif.py / dRNAas.py} -n

TIP

If pipeline broken by some error, just type command again after you fix it. snakemake will automatically continue from the broken point.