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VAST-TOOLS-NF

A Nextflow implementation of VAST-TOOLS

Quick start

Make sure you have all the required dependencies listed in the last section.

Install the Nextflow runtime by running the following command:

$ curl -fsSL get.nextflow.io | bash

When done, you can launch the pipeline execution by entering the command shown below:

$ nextflow run skptic/vast-tools-nf

By default the pipeline is executed against the provided example dataset. Check the Pipeline parameters section below to see how enter your data on the program command line.

Pipeline parameters

--reads

• Specifies the location of the reads fastq file(s).
• Multiple files can be specified using the usual wildcards (*, ?), in this case make sure to surround the parameter string value by single quote characters (see the example below)
• It must end in .fastq.
• Involved in the task: vast-tools-mapping.
• By default it is set to the VAST-TOOLS-NF's location: ./tutorial/data/*.fastq

Example:

$ nextflow run cbcrg/vast-tools-nf --reads '/home/dataset/*.fastq'

This will handle each fastq file as a seperate sample.

Read pairs of samples can be specified using the glob file pattern. Consider a more complex situation where there are three samples (A, B and C), with A and B being paired reads and C being single ended. The read files could be:

sample_A_1.fastq
sample_A_2.fastq
sample_B_1.fastq
sample_B_2.fastq 
sample_C_1.fastq

The reads may be specified as below:

$ nextflow run skptic/vast-tools-nf --reads '/home/dataset/sample_*_{1,2}.fastq'    

--output

• Specifies the folder where the results will be stored for the user.
• It does not matter if the folder does not exist.
• By default is set to VAST-TOOLS-NF's folder: ./results

Example:

$ nextflow run skptic/vast-tools-nf --output /home/user/my_results 

Cluster support

VAST-TOOLS-NF execution relies on Nextflow framework which provides an abstraction between the pipeline functional logic and the underlying processing system.

Thus it is possible to execute it on your computer or any cluster resource manager without modifying it.

Currently the following platforms are supported:

• Oracle/Univa/Open Grid Engine (SGE)
• Platform LSF
• SLURM
• PBS/Torque

By default the pipeline is parallelized by spanning multiple threads in the machine where the script is launched.

To submit the execution to a SGE cluster create a file named nextflow.config, in the directory where the pipeline is going to be launched, with the following content:

process {
  executor='sge'
  queue='<your queue name>'
}

In doing that, tasks will be executed through the qsub SGE command, and so your pipeline will behave like any other SGE job script, with the benefit that Nextflow will automatically and transparently manage the tasks synchronisation, file(s) staging/un-staging, etc.

Alternatively the same declaration can be defined in the file $HOME/.nextflow/config.

To lean more about the avaible settings and the configuration file read the Nextflow documentation.

Dependencies

• Java 7+
• Nextflow (0.18.0 or higher)
• VAST-TOOLS
• VASTDB (VAST-TOOLS Database)
• R - https://www.r-project.org/