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UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline
https://github.com/UCSF-Costello-Lab/LG3_Pipeline
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lg3 run <step> #164

Closed HenrikBengtsson closed 2 years ago

HenrikBengtsson commented 2 years ago

Background

Having to call ./_run_Align_mem is kind of tedious and "unusual". It also requires that we have linked it to the installation path, i.e. _run_Align_mem -> ${LG3_HOME}/runs_demo/_run_Align_mem.

Wish

Implement an lg3 run <step> command so that we can run it as:

$ lg3 run Align_mem

Internally, this can call ${LG3_HOME}/runs_demo/_run_Align_mem. This will allow us to drop all those symbolic ./_run_* links that clutter up the working directory.

Related

This same feature request was brought up in Issue #84. I'll close that one in favor of this one.

HenrikBengtsson commented 2 years ago

Added to the 'next-release' branch, e.g.

$ lg3 run --help
Run an LG3 Pipeline Step

Usage:
 lg3 run [options] <step> <patient> <patient2> ...

Options:
 --dryrun   Do everything but launching the run script
 --list     List all available LG3 run steps

Steps:
 Trim       
 Align_gz   
 Recal      
 Pindel     
 MutDet     
 PostMut    
 ...

Examples:
 lg3 run Trim
 lg3 run Align_gz
 lg3 run Recal
 lg3 run Pindel && lg3 run MutDet
 lg3 run PostMut