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2.0 Introduction to Session 2

This session builds on Session 1, where we explored the core features of nf-core and Nextflow and learnt the fundamental commands and options for executing nf-core pipelines:

  • nf-core is a curated set of analysis pipelines built using the workflow language Nextflow
  • nf-core pipelines are composed of a modular collection of workflows, subworkflows, and modules (processes) where each process performs a discrete analysis task
  • The run can be customised with pipeline parameters (--), Nextflow parameters (-), and custom configuration files
  • Nextflow run command starts the workflow
  • Nextflow log can be used to inspect run details

At the end of Session 1, we downloaded the nf-core/rnaseq pipeline and submitted our first run.

During Session 2, we will continue with this pipeline, using the same data from a published mouse RNAseq study. Pipeline outputs and source code will be explored, and various customisations will be applied using parameters and configuration files to provide you with hands-on experience in nf-core pipeline customisation. We will also learn about maintaining reproducibility and portability when running custom analyses.

Applying what you learn here to other nf-core workflows

While all activities in this session use the nf-core/rnaseq workflow, the customisation scenarios we explore are applicable to other nf-core workflows and do not require an understanding of RNA-seq data processing. These skills transfer to other nf-core pipelines thanks to Nextflow as a domain-specific workflow language designed to make workflows portable, and the nf-core specifications placing a strong emphasis on modularity and consistency in code and architecture.


Exercise 2.0.1 ⏱ 2 mins

  1. As described in the set up instructions, log back into your Nectar VM with VS Code

    • Type Ctrl + Shift + P to open command palette and select Remote-SSH: Connect to Host
    • Select the IP address for your VM from the drop-down list
    • Type in your provided password and hit enter

  2. Open the session2 folder created in the previous session

    • From the VS Code top menu bar, select File --> Open Folder
    • Then select the folder /home/<USERNAME>/session2 and click 'OK'
    • You will be prompted to enter your password again
    • Once authentication is successful, this will open the ~/session2 folder in the left hand filesystem explorer pane

  3. Open a new terminal

    • Select Terminal --> New Terminal from the VS Code top menu bar
    • This will open a terminal connected to the Nectar VMs within the lower half of the VS Code interface
    • Your command prompt should show that you are within the folder ~/session2