updates to flexiprep.md docs

docs/pipelines/flexiprep.md

 # Introduction
 
+# [Flexiprep](https://git.lumc.nl/biopet/biopet/tree/master/flexiprep)
+
+QC pipeline for fastq files
+
+### Commandline options
+
+| 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 |
+
+---
+
+### 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> |
+| 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.
+
+
+
+
+
 # Invocation
 
 # Example