Nextflow is a bioinformatics workflow management system that enables the development of scalable and reproducible scientific workflows. It supports deploying workflows on a variety of execution platforms. It allows the adaptation of pipelines written in the most common scripting languages.
For more information check here and here.
Select input parameters¶
To run a pipeline the user must set two parameters:
Input folder: It mounts the folder containing source code and input files.
Pipeline script: It selects the Nextflow pipeline script, which is a
.nffile containing the workflow instructions.
For information on how to use the Initialization parameter, please refer to the Initialization - Bash script, Initialization - Conda packages, and Initialization - pip packages section of the documentation.
Create a Conda environment¶
The user can also install the required software dependencies via Conda by specifying the packages or the path(s) to the configuration YAML file(s) directly in the pipeline script. In this case the user must use the option
Import a configuration file¶
The parameter Configuration is used to upload a Nextflow configuration file. The latter is a simple text file containing a set of properties defined using the syntax:
name = value
More information about configuration settings in Nextflow can be found in the official documentation.
The Interactive mode parameter is used to start an interactive job session where the user can open a terminal window from the job progress page and execute shell commands.