Commit 288b6bf2 authored by sajvanderzeeuw's avatar sajvanderzeeuw

docs added

parent 731d6089
......@@ -52,7 +52,7 @@ java -jar Biopet(version).jar (pipeline of interest) (pipeline options) -qsub* -
~~~
java -jar Biopet(version).jar (pipeline of interest) (pipeline options)
~~~
If one performs a dry run the config report will be generated. From this config report you can identify all configurable options.
### Shark Compute Cluster specific
......@@ -93,10 +93,6 @@ There are multiple configs that can be passed to a pipeline, for example the sam
- [Here](config) one can find how to create a sample and settings config
- More info can be found here: [How To! Config](https://git.lumc.nl/biopet/biopet/wikis/Config)
### Running a tool
$ biopet tool <tool_name>
......
Public release:
~~~bash
Biopet is built on top of GATK Queue for building bioinformatic
pipelines. It is mainly intended to support LUMC SHARK cluster which is running
SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
should also be able to execute Biopet tools and pipelines.
Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
Contact us at: sasc@lumc.nl
A dual licensing mode is applied. The source code within this project that are
not part of GATK Queue is freely available for non-commercial use under an AGPL
license; For commercial users or users who do not want to follow the AGPL
license, please contact us to obtain a separate license.
~~~
Private release:
~~~bash
Due to the license issue with GATK, this part of Biopet can only be used inside the
LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
on how to use this protected part of biopet or contact us at sasc@lumc.nl
~~~
Copyright [2013-2014] [Sequence Analysis Support Core](https://sasc.lumc.nl/)
# Introduction
# Flexiprep
# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/develop/public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep)
## Introduction
Flexiprep is out quality control pipeline. This pipeline checks for possible barcode contamination, clips reads, trims reads and runs
the tool <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">Fastqc</a>.
The adapter clipping is performed by <a href="https://github.com/marcelm/cutadapt" target="_blank">Cutadapt</a>.
For the quality trimming we use: <a href="https://github.com/najoshi/sickle" target="_blank">Sickle</a>. Flexiprep works on `.fastq` files.
QC pipeline for fastq files
### Commandline options
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0-DEV.jar pipeline Flexiprep -h
Arguments for Flexiprep:
-R1,--input_r1 <input_r1> R1 fastq file (gzipped allowed)
-sample,--samplename <samplename> Sample name
-library,--libraryname <libraryname> Library name
-outDir,--output_directory <output_directory> Output directory
-R2,--input_r2 <input_r2> R2 fastq file (gzipped allowed)
-skiptrim,--skiptrim Skip Trim fastq files
-skipclip,--skipclip Skip Clip fastq files
-config,--config_file <config_file> JSON config file(s)
-DSC,--disablescatterdefault Disable all scatters
~~~
| Argument | Explain |
| -------- | ------- |
| -R1,--input_r1 <input_r1> | R1 fastq file (gzipped allowed) |
| -outputDir,--outputdir <outputdir> | Output directory |
| -config,--configfiles <configfiles> | Config Json file |
| -R2,--input_r2 <input_r2> | R2 fastq file (gzipped allowed) |
| -skiptrim,--skiptrim | Skip Trim fastq files |
| -skipclip,--skipclip | Skip Clip fastq files |
As we can see in the above example we provide the options to skip trimming or clipping
since sometimes you want to have the possibility to not perform these tasks e.g.
if there are no adapters present in your .fastq. Note that the pipeline also works on unpaired reads where one should only provide R1.+
---
### Config options
To start the pipeline (remove `-run` for a dry run):
~~~bash
java -jar Biopet-0.2.0.jar pipeline Flexiprep -run -outDir myDir \
-R1 myFirstReadPair -R2 mySecondReadPair -sample mySampleName \
-library myLibname -config mySettings.json
~~~
| 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 | skiptrim | Boolean | false | |
| flexiprep | skiptrim | Boolean | false | |
---
### 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 |
| ----------- | ---- | ---- | ------- | -------- |
| cutadapt | exe | String | cutadapt | Excuteble for cutadapt |
| cutadapt | default_clip_mode | String | 3 | Do not make a link with name: <sample>.qc.<fastq extension> |
| cutadapt | adapter | Array[String] | | |
| cutadapt | anywhere | Array[String] | | |
| cutadapt | front | Array[String] | | |
| cutadapt | discard | Boolean | false | |
| cutadapt | opt_minimum_length | Int | 1 | |
| cutadapt | opt_maximum_length | Int | | |
| fastqc | exe | String | fastqc | Excuteble for fastqc |
| fastqc->java | kmers | String | java | Excuteble for java for fastqc |
| fastqc | kmers | Int | 5 | |
| fastqc | quiet | Boolean | false | |
| fastqc | noextract | Boolean | false | |
| fastqc | nogroup | Boolean | false | |
| sickle | exe | String | sickle | Excuteble for sickle |
| sickle | qualitytype | String | | |
| sickle | defaultqualitytype | String | sanger | use this when quality type can't be found at fastqc |
---
### License
A dual licensing model is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact sasc@lumc.nl to purchase a separate license.
# Example
Note that one should first create the appropriate [configs](../config.md).
# Testcase A
# Testcase B
# Examine results
......
......@@ -52,9 +52,11 @@ Arguments for Mapping:
To run the pipeline:
~~~
java -jar Biopet.0.2.0.jar pipeline mapping -run --config mySamples.json --config mySettings.json
java -jar Biopet.0.2.0.jar pipeline mapping -run --config mySettings.json \
-R1 myReads1.fastq -R2 myReads2.fastq -outDir myOutDir -OutputName myReadsOutput \
-R hg19.fasta -RGSM mySampleName -RGLB myLib1
~~~
__Note that the pipeline also accepts sample specification through command line but we encourage you to use the sample config__
Note that removing -R2 causes the pipeline to be able of handlind single end `.fastq` files.
To perform a dry run simply remove `-run` from the commandline call.
......
......@@ -6,13 +6,15 @@ The Sage pipeline has been created to process SAGE data, which requires a differ
* [Flexiprep](flexiprep.md)
* [Mapping](mapping.md)
* [SageCountFastq](sagetools.md)
* [SageCreateLibrary](sagetools.md)
* [SageCreateTagCounts](sagetools.md)
* [SageCountFastq](../tools/sagetools.md)
* [SageCreateLibrary](../tools/sagetools.md)
* [SageCreateTagCounts](../tools/sagetools.md)
# Example
Note that one should first create the appropriate [configs](../config.md).
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar pipeline Sage -h
Arguments for Sage:
......@@ -25,6 +27,11 @@ Arguments for Sage:
-DSC,--disablescatterdefault Disable all scatters
~~~
To run the pipeline:
~~~
java -jar Biopet-0.2.0-DEV-801b72ed.jar pipeline Sage -run --config MySamples.json --config --MySettings.json
~~~
# Examine results
......
# BedToInterval
## Introduction
BedToInterval has been written to ensure a proper input for the tools from Picard.
Since the latest release of Picard tools (v 1.124) there is already a tool available called: BedToIntervalList.
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0.jar tool BedToInterval -h
Usage: BedToInterval [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-I <file> | --inputFile <file>
-o <file> | --output <file>
-b <file> | --bam <file>
~~~
To run the tool:
~~~
java -jar Biopet-0.2.0 tool BedToInterval -I myBed.bed -o myIntervals.txt -b myBam.bam
~~~
## Results
The results of this tool will be a tab delimited text file called a interval list.
\ No newline at end of file
# BedtoolsCoverageToCounts
## Introduction
This tool enables a user to generate a count file, out of a coverage file.
## Example
To get the help menu:
~~~bash
java -jar Biopet-0.2.0.jar tool BedtoolsCoverageToCounts -h
Usage: BedtoolsCoverageToCounts [options]
-l <value> | --log_level <value>
Log level
-h | --help
Print usage
-v | --version
Print version
-I <file> | --input <file>
-o <file> | --output <file>
~~~
input: coverage file produced with bedtools
output: a count file with the counts from the the values inside the coverage file. Where values could be almost everything, e.g.
genes, ensemblIDs etc. etc.
To run the tool:
~~~bash
java -jar Biopet-0.2.0.jar tool BedtoolsCoverageToCounts
~~~
\ No newline at end of file
# SAGE tools
These tools are written to create the appropriate files for the SAGE pipeline.
Note that these tools are already implemented in the pipeline.
## SageCountFastq
~~~
java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
Usage: SageCountFastq [options]
-l <value> | --log_level <value>
......@@ -18,6 +20,7 @@ Usage: SageCountFastq [options]
## SageCreateLibrary
~~~
java -jar Biopet-0.2.0.jar tool SageCreateLibrary -h
Usage: SageCreateLibrary [options]
-l <value> | --log_level <value>
......@@ -44,6 +47,7 @@ Usage: SageCreateLibrary [options]
## SageCreateTagCounts
~~~
java -jar Biopet-0.2.0.jar tool SageCreateTagCounts -h
Usage: SageCreateTagCounts [options]
-l <value> | --log_level <value>
......
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