Introduction to Session 2¶
Session 2 builds on fundamental concepts learned in Session 1 and provides you with hands-on experience in nf-core pipeline customisation.
We will explore the pipeline source code and apply various customisations using a parameter file and custom configuration files. You will:
- Explore the nf-core/sarek source code
- Create custom input files and customise the pipeline execution
- Review the execution of the pipeline with the customisations applied
Each lesson in this session will build on previous lessons. By the end of this session you will have a deeper understanding of the customisation techniques and the impact they have on the pipeline execution.
Applying what you learn
Although activities in this session will use version 3.2.3 of the nf-core/sarek pipeline, all customisation scenarios we explore are applicable to other nf-core pipelines.
Log back in into NESI¶
Follow set up instructions to log back into Nesi.
Load modules and activate the nf-core conda environment¶
If your previous session has ended you may need to load the required modules and activate the nf-core conda environment again by running the following source command