README.md

# Code Club: Gentle Introduction to Snakemake

## Exercises

### Exercise ex1:

Write a Snakemake rule __generate_data__ using Python language to generate two vectors of random numbers of size 100 and save each vector to a separate text file: _x.txt_ and _y.txt_.

  **Hint 1.** Import numpy library
  
   ```{py}
  import numpy as np
  ```
  
  **Hint 2.** Define the names of the output files before the rules
  
  ```{py}
  file_ids = ['x', 'y']
  ```
  
  **Hint 3.** Use special Snakemake function to create a list of output filenames from a pattern (for example, in the rule all)
  
  ```{}
  expand("data/{file}.txt", file = file_ids)
  ```
___

### Exercise ex2:

Write a snakemake rule **subset_data** using shell to create two subsets from the generated files, so that each new file will contain the value less or equal to **0.5**. Save each new generated vector to a separate text file: _x_subset.txt_ and _y_subset.txt_.

  **Hint 1.** Use the ```awk``` shell command to subset the data and ```>``` to redirect the output:
  ```{sh}
  awk ‘$1 <= 0.5’ {input} > {output}
  ```
____
 
### Exercise ex3:
 
Write a snakemake rule using the custom R script (scripts/plot.R) to plot two vectors generated in the **ex2**. 
____
 
### Exercise ex4:
 
Combine all rules into one pipeline, delete all before generated files and run the whole pipeline again specifying the final output.