Commit de1e58d8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added tags documentation

parent c0d95004
......@@ -47,16 +47,24 @@ For BAM files as input one should use a config like this:
``` yaml
samples:
Sample_ID_1:
tags:
gender: male
father: sampleNameFather
mother: sampleNameMother
libraries:
Lib_ID_1:
tags:
key: value
bam: MyFirst.bam
Lib_ID_2:
bam: MySecond.bam
```
Note that there is a tool called [SamplesTsvToJson](../tools/SamplesTsvToJson.md) this enables a user to get the sample config without any chance of creating a wrongly formatted JSON file.
#### Tags
In the `tags` key inside a sample or library users can supply tags die samples. This tags will we automaticly parsed inside the summary of a pipeline.
### The settings config
The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
......
......@@ -21,12 +21,18 @@ Usage: SamplesTsvToJson [options]
Print version
-i <file> | --inputFiles <file>
Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed
-t <file> | --tagFiles <file>
-o <file> | --outputFile <file>
~~~
The tool is designed in such a way that a user can provide a TAB seperated file (TSV) with sample specific properties and even those will be parsed by the tool.
For example: a user wants to have certain properties e.g. which treatment a sample got than the user should provide a extra columns called treatment and then the
JSON file is parsed with those properties inside it as well. The order of columns does not matter.
The tag files works the same only the value are prefixed in the key `tags`.
#### Example
~~~ json
......
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