Assignment III

Your main.nf script should be able to perform FASTQC and MULTIQC on your sequencing data.

I have added a process called TX - which generates a transcriptome FASTA file for Kallisto.

Update your main.nf script to include:

  1. Transcriptome Indexing.

  2. Kallisto Quantification.

Refer to the Kallisto documentation and inspect the kalisto index and kallisto quant commands.

Before designing a nextflow workflow, you need to be familiar with the expected outputs generated by the process script body. Shell into your container to run the quantification analysis in bash before implementing the process in nextflow.

Template script

I have a heavily commented template script for you to use as a starting point: https://github.com/BarryDigby/rtp_workshop2/blob/dev/template.nf

DAG

Hopefully the dag gives you clues how to proceed,.,.,.,.??

../_images/flowchart.png

Advanced script

As it stands, your main.nf script will run each process every time we run it. We want to make use of conditional statements to allow users to skip processes - saving computational time and resources.

Refer to the Condtionals documentation - I have included appropriate parameters and code in both our nextflow.config and main.nf scripts for quality control and generating the transcriptome file.

Your task is to:

  • Include 2 boolean parameters kallisto_index and save_index in your nextflow.config file and script. Use these in a similar fashion to the transcriptome and save_transcriptome parameters in the documentation.

We do not need any condional statements for the quantification step - we want to run this every time.

Please ask for help if anything is unclear.