From b662fcf5f77cac7d6c350e5e4ab7e8b237c2539f Mon Sep 17 00:00:00 2001 From: Sander Bollen <a.h.b.bollen@lumc.nl> Date: Tue, 9 Jun 2015 12:08:05 +0200 Subject: [PATCH] flexiprep requirements --- docs/pipelines/flexiprep.md | 60 +++++++++++++++++++++++++------------ 1 file changed, 41 insertions(+), 19 deletions(-) diff --git a/docs/pipelines/flexiprep.md b/docs/pipelines/flexiprep.md index 56da30f1f..613b53463 100644 --- a/docs/pipelines/flexiprep.md +++ b/docs/pipelines/flexiprep.md @@ -1,32 +1,29 @@ # 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 -- GitLab