Nextflow

Nextflow type access

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Nextflow type access

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.

Select input parameters

The app has two mandatory parameters:

  • Input folder: it mounts the folder containing source code and input files.

  • Pipeline script: it selects the Nextflow pipeline script, which is a .nf file containing the workflow instructions.

Additional Dependencies

For information on how to use the Additional dependencies 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 specifyifg 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 -with-conda.

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.

Interactive mode

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.