Name: grape-nf
Owner: Notredame Lab
Description: Yet another Grape RNA-Seq analyses pipeline
Created: 2013-06-27 12:52:49.0
Updated: 2016-01-28 13:01:16.0
Pushed: 2015-01-01 23:50:37.0
Size: 69279
Language: Shell
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Yet another Grape pipeline implementation
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 cbcrg/grape-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.
–genome
$ nextflow run cbcrg/grape-nf --genome /home/user/my_fastas/example.fa–annotation
$ nextflow run cbcrg/grape-nf --annotation /users/bm/notes.gtf–primary
$ nextflow run cbcrg/grape-nf --primary '/home/dataset/*_1.fastq'–secondary
$ nextflow run cbcrg/grape-nf --secondary '/home/dataset/*_2.fastq'–quality
$ nextflow run cbcrg/grape-nf --quality 64–cpus
$ nextflow run cbcrg/grape-nf --cpus 10–output
$ nextflow run cbcrg/grape-nf --output /home/user/my_results–mapper
gem and tophat2.gem$ nextflow run cbcrg/grape-nf --mapper tophat2Grape-NF dependecies are also distributed by using a Docker container which frees you from the installation and configuration of all the pieces of software required by Grape-NF.
The Grape-NF Docker image is published at this address https://registry.hub.docker.com/u/cbcrg/grape-nf/
If you have Docker installed in your computer pull this image by entering the following command:
$ docker pull cbcrg/grape-nf
After that you will be able to run Grape-NF using the following command line:
$ nextflow run cbcrg/grape-nf -with-docker --mapper tophat2
Note: currently Docker based installation only support Tophat.
Grape-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 clusters are supported:
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:
task {
processor='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 http://www.nextflow.io/docs/latest/config.html
When using Tophat as mapper