Getting started with Snakemake
It’s the same setup as for Exercise 1A and Exercise 1B: we will work on a node of the cluster with Snakemake, FastQC and MultiQC modules loaded.
As a reminder, you should be in your working directory from Exercise 1A and B in which you have the Data/ folder containing all example files.
john.doe@node06:/data/work/I2BC/john.doe/snakemake_tutorial$ ls -a
. .. .snakemake Data FastQC multiqc_data multiqc_report.html
You should also have snakemake, FastQC and MultiQC loaded.
john.doe@node06:/data/work/I2BC/john.doe/snakemake_tutorial$ fastqc --version
FastQC v0.11.5
john.doe@node06:/data/work/I2BC/john.doe/snakemake_tutorial$ snakemake --version
8.4.6
john.doe@node06:/data/work/I2BC/john.doe/snakemake_tutorial$ multiqc --version
multiqc, version 1.9
NB: If you’re starting Exercise 1 from here, you can copy the solution script ex1b_o3.smk from Exercise 1B objective 3.