Add new flag to `snappy-start-project`

eudesbarbosa commented 3 years ago

New feature

Add new flag --germline-example to snappy-start-project. Usage:

snappy-start-project --directory PATH_TO_PROJECT --germline-example

Expected behaviour

Script should setup directory simplified version of use case described in #10, only:

ngs_mapping
variant_calling

Directory should contain all files required to run a simple analysis (expect for conda envs), that includes:

All required directories;
Config file with all required parameters set;
Small example based on GIAB;
Tour over directory and file structure (bonus).

holtgrewe commented 3 years ago

I'd rather have users fork & clone a repository than embed this into the manual. What do you think about that path forward? Less code...

eudesbarbosa commented 3 years ago

I was more aiming for an "instant gratification" step. By the time the user would arrive at this point, they would have went through 2-3 pages from readthedocs, it would be nice to see that the installation, etc worked.

Plus, if things go well in #10, it won't be hard to revamp it into a new class in the main code.

bihealth / snappy-pipeline

Add new flag to `snappy-start-project` #46