Commit eb74d901 authored by sajvanderzeeuw's avatar sajvanderzeeuw

changes in docs

parent 5e556be9
# How to create configs
### The Sample config
### The sample config
The sample config should be in [__JSON__](http://www.json.org/) format
- First field should have the key __"samples"__
- Second field should contain the __"libraries"__
- Third field contains __"R1" or "R2"__ or __"bam"__
- The fastq input files can be provided zipped and un zipped
~~~
{
"samples":{
"Sample_ID1":{
"libraries":{
"MySeries_1":{
"R1":"Youre_R1.fastq.gz",
"R2":"Youre_R2.fastq.gz"
}
}
}
}
}
~~~
- For BAM files as input one should use a config like this:
~~~
{
"samples":{
"Sample_ID_1":{
"libraries":{
"Lib_ID_1":{
"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.
### 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.
\ No newline at end of file
......@@ -6,6 +6,7 @@ QC pipeline for fastq files
### Commandline options
| Argument | Explain |
| -------- | ------- |
| -R1,--input_r1 <input_r1> | R1 fastq file (gzipped allowed) |
......@@ -19,6 +20,7 @@ QC pipeline for fastq files
### Config options
| Config Name | Name | Type | Default | Function |
| ----------- | ---- | ----- | ------- | -------- |
| flexiprep | skip_native_link | Boolean | false | Do not make a link to the final file with name: <sample>.qc.<fastq extension> |
......@@ -29,6 +31,7 @@ QC pipeline for fastq files
### sub Module options
This can be used in the root of the config or within the flexiprep, within flexiprep got prio over the root value
| Config Name | Name | Type | Default | Function |
......
This tool enables a user to create a full sample sheet in JSON format suitable for all our Queue pipelines.
The tool can be started as follows:
~~~
java -Xmx2G -jar Biopet-0.2.0.jar tool SamplesTsvToJson
~~~
__-Xmx2G__ defines the amount of memory used to run the tool. Usually one should not change this value since 2G is more than enough.
~~~
Usage: SamplesTsvToJson [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
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
~~~
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.
#### Example
~~~
{
"samples" : {
"Sample_ID_1" : {
"treatment" : "heatshock",
"libraries" : {
"Lib_ID_1" : {
"bam" : "MyFirst.bam"
}
}
},
"Sample_ID_2" : {
"treatment" : "heatshock",
"libraries" : {
"Lib_ID_2" : {
"bam" : "MySecond.bam"
}
}
}
}
}
~~~
#### Sample definition
To get the above example out of the tool one should provide 2 TSV files as follows:
----
| samples | library | bam |
| ------- | ------- | --------- |
|Sample_ID_1 |Lib_ID_1 |MyFirst.bam |
|Sample_ID_2 |Lib_ID_2 |MySecond.bam |
----
#### Library definition
The second TSV file can contain as much properties as you would like. Possible option would be: gender, age and family.
Basically anything you want to pass to your pipeline is possible.
----
| sample | treatment |
| ----------- | --------- |
| Sample_ID_1 | heatshock |
| Sample_ID_2 | heatshock |
site_name: Biopet
site_name: Biopet user manual
pages:
- ['index.md', 'Home']
- ['config.md', 'Config']
- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['pipelines/basty.md', 'Pipelines', 'Basty']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
......
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