pgx-nf

Quick Start

The pipeline can be run on:

• the command line
• Deploit (recommended)

Running on the command line

Dependencies

Nextflow Docker

As all of the available parameters can already be found within the nextflow.config file, an example run of the pipeline on the pipeline may look like this:

nextflow run lifebit-ai/pgx-nf

You can change the input parameters by either changing them in the nextflow.config file or specifying them on the command line eg:

nextflow run main.nf --celllines testdata/annotation/cell_annotation_all.csv

Deploit

Deploit is a bioinformatics platform, developed by Lifebit, where you can run your analysis over the Cloud/AWS.

It is free for indivudal users to sign-up

To run the pipeline once logged in navigate to the pipelines page:

Import the pipeline

To import the pipeline into Deploit you simply need to copy & paste the GitHub repository URL: https://github.com/lifebit-ai/pgx-nf. To do so follow the steps below:

Running on Deploit

The pipeline can then be run in three simple steps:

1. Find & select the pipeline After importing the pipeline into Deploit you are immediately taken to the input data & parameters page and so might not need to do this. Imported pipelines are found under the MY PIPELINES & TOOLS section. The name with be the same as you used to import the pipeline, eg pgx-nf.
2. Enter the data & parameters here you can specify the input parameters & data. You may not need specify any parameters as they are already provided in the nextflow.config file. However, you can overwrite the parameters in the config file by specifying parameters on Deploit
3. Select a project & instance before running the analysis you must select the instance. This determines the available resources & cost. The project allows multiple jobs to be grouped together/organised

See an example execution of the pipeline on Deploit: