Commit 2ac12ea5 authored by Sander Bollen's avatar Sander Bollen
Browse files

Use namespace terminology (see #163)

parent 5b1fc7c4
......@@ -95,15 +95,15 @@ To view all possible config options please navigate to our Gitlab wiki page
<a href="https://git.lumc.nl/biopet/biopet/wikis/GATK-Variantcalling-Pipeline" target="_blank">Config</a>
### Required settings
| Config Name | Name | Type | Default | Function |
| Namespace | Name | Type | Default | Function |
| ----------- | ---- | ---- | ------- | -------- |
| | output_dir | String | | Path to output directory |
| - | output_dir | String | | Path to output directory |
| Shiva | variantcallers | List[String] | | Which variant callers to use |
### Config options
| Config Name | Name | Type | Default | Function |
| Namespace | Name | Type | Default | Function |
| ----------- | ---- | ----- | ------- | -------- |
| shiva | reference | String | | reference to align to |
| shiva | dbsnp | String | | vcf file of dbsnp records |
......@@ -136,7 +136,7 @@ The other mode, `library_variantcalling`, will call simultaneously call all libr
The config for these therefore is:
| Config Name | Name | Type | Default | Function |
| Namespace | Name | Type | Default | Function |
| ----------- | ---- | ---- | ------- | -------- |
| shiva | multisample_variantcalling | Boolean | true | Default, multisample calling |
| shiva | single_sample_variantcalling | Boolean | false | Not-recommended, single sample, merged bam |
......
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