docs added

288b6bf2 · sajvanderzeeuw · 731d6089 · 288b6bf2 · 288b6bf2 · 288b6bf2
Commit 288b6bf2 authored Dec 05, 2014 by sajvanderzeeuw
--- a/docs/index.md
+++ b/docs/index.md
@@ -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>

--- a/docs/license.md
+++ b/docs/license.md
+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/)
--- a/docs/pipelines/flexiprep.md
+++ b/docs/pipelines/flexiprep.md
-# 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


--- a/docs/pipelines/mapping.md
+++ b/docs/pipelines/mapping.md
@@ -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.


--- a/docs/pipelines/sage.md
+++ b/docs/pipelines/sage.md
@@ -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


--- a/docs/tools/bedtointerval.md
+++ b/docs/tools/bedtointerval.md
+# 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
--- a/docs/tools/bedtoolscoveragetocounts.md
+++ b/docs/tools/bedtoolscoveragetocounts.md
+# 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
--- a/docs/tools/sagetools.md
+++ b/docs/tools/sagetools.md
 # 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>