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Peter van 't Hof authoredPeter van 't Hof authored
- Flexiprep
- Commandline options
- 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: .qc. | | flexiprep | skiptrim | Boolean | false | | | flexiprep | skiptrim | Boolean | false | |
- sub Module options
- | 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: .qc. | | 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
README.md 2.12 KiB
Flexiprep
QC pipeline for fastq files
Commandline options
- -R1,--input_r1 <input_r1> -- R1 fastq file (gzipped allowed)
- -outputDir,--outputdir -- Output directory
- -config,--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: .qc. | | 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: .qc. | | 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.