# Flexiprep

QC pipeline for fastq files

### Commandline options
- -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 |
| :- | :- | :- | :- |
| cutadept | exe |  String | cutadapt | Excuteble for cutadapt |
| cutadept | default_clip_mode |  String | 3 | Do not make a link with name: <sample>.qc.<fastq extension> |
| cutadept | adapter |  Array[String] |  |  |
| cutadept | anywhere |  Array[String] |  |  |
| cutadept | front |  Array[String] |  |  |
| cutadept | discard |  Boolean | false |  |
| cutadept | opt_minimum_length |  Int | 1 |  |
| cutadept | 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 mode 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.