RefChef creates folders to store your references. The names of these folders is based on:

  1. The master.yaml key (which should match the 'name' entry under 'metadata' in master.yaml).

  2. The 'component' entry under 'levels' in master.yaml.

Here is the collapsed file tree that refchef created from the Tutorial part of the documentation and what the directory names are based on:

./Users/jwalla12/references #this directory is specified in refchef-cook or the config files
└── S_cerevisiae            #this is named after the 'key' and the 'name' entry under 'metadata' in master.yaml
    ├── bowtie2_index       #this folder is created in the master.yaml `commands` section.
    ├── bwa_index           #this folder is created in the master.yaml `commands` section.
    ├── gtf                 #this folder is created in the master.yaml `commands` section.
    └── primary             #this is named after the 'component' entry under 'levels' in master.yaml

Here is the expanded file tree:

└── S_cerevisiae      
    ├── bowtie2_index 
    │   └── metadata.txt
    ├── bwa_index     
    │   └── metadata.txt
    ├── gtf          
    │   ├── CHECKSUMS
    │   ├── Saccharomyces_cerevisiae.R64-1-1.87.gtf
    │   ├── final_checksums.md5
    │   ├── metadata.txt
    │   └── postdownload-checksums.md5
    └── primary      
        ├── CHECKSUMS
        ├── Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
        ├── bowtie2_index -> /Users/jwalla12/references/S_cerevisiae/bowtie2_index
        ├── bwa_index -> /Users/jwalla12/references/S_cerevisiae/bwa_index
        ├── final_checksums.md5
        ├── metadata.txt
        └── postdownload-checksums.md5

This indicates that refchef has created symlinked directories for bowtie2 and bwa indices in /Users/jwalla12/references/S_cerevisiae/primary. This process (linking reference and index) is triggered by: 1. The addition of the src: line in bowtie2.yaml and bwa.yaml 2. Specifying the master.yaml levels are indices: in the master.yaml

If we look at the output from refchef-menu, we see the UUID for the primary reference file, which is dff337a6-9a1d-3313-8ced-dc6f3bfc9689.

┌ 🐶 RefChef Menu ────────────────────────┬───────────┬───────────────────────────────────────────┬──────────────────────────────────────┐
│ name         │ organism                 │ component │ description                               │ uuid                                 │
│ S_cerevisiae │ Saccharomyces cerevisiae │ primary   │ corresponds to ganbank id GCA_000146045.2 │ dff337a6-9a1d-3313-8ced-dc6f3bfc9689 │

In this clipping from bowtie2.yaml, note that the UUID was indicated in the src: entry under component, indices, and levels.

    - component: bowtie2_index
        status: false
      src: dff337a6-9a1d-3313-8ced-dc6f3bfc9689 

This indicates which primary reference was used to create the index file.