Commit b662fcf5 authored by Sander Bollen's avatar Sander Bollen
Browse files

flexiprep requirements

parent 9bf8beff
# 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.
Flexiprep is our quality control pipeline. This pipeline checks for possible barcode contamination, clips reads, trims reads and runs
the <a href="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" target="_blank">Fastqc</a> tool.
Adapter clipping is performed by <a href="https://github.com/marcelm/cutadapt" target="_blank">Cutadapt</a>.
For quality trimming we use <a href="https://github.com/najoshi/sickle" target="_blank">Sickle</a>.
Flexiprep works on `.fastq` files.
## Example
To get the help menu:
~~~
java -jar Biopet-0.2.0-DEV.jar pipeline Flexiprep -h
java -jar </path/to/biopet.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
-R1,--input_r1 <input_r1> R1 fastq file (gzipped allowed)
-R2,--input_r2 <input_r2> R2 fastq file (gzipped allowed)
-sample,--sampleid <sampleid> Sample ID
-library,--libid <libid> Library ID
-config,--config_file <config_file> JSON config file(s)
-DSC,--disablescatter Disable all scatters
~~~
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.
Note that the pipeline also works on unpaired reads where one should only provide R1.
To start the pipeline (remove `-run` for a dry run):
......@@ -36,9 +33,34 @@ java -jar Biopet-0.2.0.jar pipeline Flexiprep -run -outDir myDir \
-library myLibname -config mySettings.json
~~~
## Configuration and flags
For technical reasons, single sample pipelines, such as this pipeline do **not** take a sample config.
Input files are in stead given on the command line as a flag.
Command line flags for Flexiprep are:
| Flag (short)| Flag (long) | Type | Function |
| ------------ | ----------- | ---- | -------- |
| -R1 | --input_r1 | Path (**required**) | Path to input fastq file |
| -R2 | --input_r2 | Path (optional) | Path to second read pair fastq file. |
| -sample | --sampleid | String (**required**) | Name of sample |
| -library | --libid | String (**required**) | Name of library |
If `-R2` is given, the pipeline will assume a paired-end setup.
### Config
All other values should be provided in the config. Specific config values towards the mapping pipeline are:
| Name | Type | Function |
| ---- | ---- | -------- |
| skiptrim | Boolean | Skip the trimming step |
| skipclip | Boolean | Skip the clipping step |
## Result files
The results from this pipeline will be a fastq file which is depending on the options either clipped and trimmed, only clipped,
only trimmed or no quality control at all. The pipeline also outputs 2 Fastqc runs one before and one after quality control.
The results from this pipeline will be a fastq file.
The pipeline also outputs 2 Fastqc runs one before and one after quality control.
### Example output
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment