Welcome
In Part 1 of this workshop, you will create a toy multi-step Nextflow workflow.
We will start Part 1 by familiarizing ourselves with some common bash commands. Next, we will turn these commands into a small single-step Nextflow pipeline that will print a greeting to our terminal. In a series of exercises, we will then iterate on this pipeline to make it more flexible using variable outputs, inputs, and parameters. Finally, we will add a second step to the pipeline to dynamically turn our greeting into uppercase letters and name pipeline outputs.
During Part 2, the skills and concepts you have learned in Part 1 will be applied in a more realistic scenario.
Moving into your work directory
It is good practice to organize projects into their own folders to make it easier to track and replicate experiments over time.
We have created separate directories for each part (~/part1/ and ~/part2/).