Entry Points Sub-workflow¶
- Workflow File:
Config Options: see The config.yml for more details
user_files.gtc_pattern
user_files.idat_pattern
user_files.ped
user_files.map
user_files.bed
user_files.bim
user_files.fam
Major Outputs:
sample_level/samples.bed
sample_level/samples.bim
sample_level/samples.fam
There are three paths we can take to create these files:
If GTC files are provided using
user_files.gtc_pattern
then we will
![../_images/entry-points_gtc.png](../_images/entry-points_gtc.png)
Fig. 2 The GTC entry-point workflow. If per sample GTC files are provided, then we will convert these files to the PED/MAP format and merge them together.¶
If an aggregated PED/MAP is provided using
user_files.ped
anduser_files.map
then we will convert the PED/MAP to BED/BIM/FAM.If an aggregated BED/BIM/FAM is provided using
user_files.bed
,user_files.bim
,user_files.fam
then we will create a symbolic link.