Snakefile_workflow1

# This first line is used to save the snake code below into a file called "Snakefile"

######################################################################################
####################### Content of the Snakefile #####################################
### Import some useful python library and some needed lines of code ###
import os
root = os.getcwd() # or copy here the path to the delatres_snakemake folder eg root = r"d:\repos\deltares_snakemake"

### Parse config options ###
LINE1 = config["line1"]
LINE2 = config["line2"]

### Worflow and rules ###
# Master rule all (needed when several rules are defined, called all by convention)
rule all:
    input: root + "/output/snake2.txt"

# Rule to create a text file
rule create_file:
    output: root + "/data/snake.txt"
    params:
        line1 = LINE1,
        line2 = LINE2
    script:
        "scripts/create_file.py"

# Rule to copy a file in Windows
rule run_copy_file:
    input: root + "/data/snake.txt"
    output: root + "/output/snake.txt"
    shell:
        """copy "data\snake.txt" "output\snake.txt" """

# Rule to rename a file
rule rename_file:
    input: root + "/output/snake.txt"
    output: root + "/output/snake2.txt"
    shell:
        """ren "output\snake.txt" "snake2.txt" """