[x] categorize inputs, outputs from each rule (provide options, e.g. either raw reads or trimmed reads)
[x] add a "help" key to params.yml. Use this to print some helpful info about how to use the program/rule (perhaps type of input/output, or workflows that rule is currently in, etc).
[x] add "citation" key to params.yml. For future use printing citations of programs used in a workflow.
B. checks for input config files (+ maybe tsv files?):
[x] write json schema for the config.yaml that will check formatting. Catch improperly formatted yaml configs and try to be helpful. To do this:
[x] script to generate yaml schema for default params for each rule file
[x] aggregate these schema for included rules in order to check that input config is correct
[x] use snakemake validate to check? Or otherwise validate!
[x] modify "required" in schema to match current targets. To do this, generate new full schema as a process in __main__.
[x] for samples file (specified in config.yml), check that files can be found:
Implement some input/output checks (#110):
A. rule inputs/outputs
params.yml. Use this to print some helpful info about how to use the program/rule (perhaps type of input/output, or workflows that rule is currently in, etc).params.yml. For future use printing citations of programs used in a workflow.B. checks for input
configfiles (+ maybetsvfiles?):yamlconfigs and try to be helpful. To do this:__main__.