Commit eb74d901 authored by sajvanderzeeuw's avatar sajvanderzeeuw
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changes in docs

parent 5e556be9
# How to create configs # 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 ...@@ -6,6 +6,7 @@ QC pipeline for fastq files
### Commandline options ### Commandline options
| Argument | Explain | | Argument | Explain |
| -------- | ------- | | -------- | ------- |
| -R1,--input_r1 <input_r1> | R1 fastq file (gzipped allowed) | | -R1,--input_r1 <input_r1> | R1 fastq file (gzipped allowed) |
...@@ -19,6 +20,7 @@ QC pipeline for fastq files ...@@ -19,6 +20,7 @@ QC pipeline for fastq files
### Config options ### Config options
| Config Name | Name | Type | Default | Function | | 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> | | 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 ...@@ -29,6 +31,7 @@ QC pipeline for fastq files
### sub Module options ### 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 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 | | 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: pages:
- ['index.md', 'Home'] - ['index.md', 'Home']
- ['config.md', 'Config']
- ['tools/SamplesTsvToJson.md','tools','SamplesTsvToJson']
- ['pipelines/basty.md', 'Pipelines', 'Basty'] - ['pipelines/basty.md', 'Pipelines', 'Basty']
- ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep'] - ['pipelines/flexiprep.md', 'Pipelines', 'Flexiprep']
- ['pipelines/gentrap.md', 'Pipelines', 'Gentrap'] - ['pipelines/gentrap.md', 'Pipelines', 'Gentrap']
......
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