Snakefile

import os

stream = os.popen('tail -1 data/input.txt')
output = int(stream.read())

scattergather:
    split=output


# keep me at the top
rule all:
    input:
        "results/final_output.txt"

# takes one input, produces one output 
rule first_rule:
    input:
        "data/input.txt"
    output:
        "intermediate/single_output.txt"
    shell:
        "workflow/your_script --input {input} --output {output}"

# takes one input, expands to a directory of outputs
rule second_rule:
    input:
        "intermediate/single_output.txt"
    output:
        scatter.split("intermediate/multiple_outputs/{scatteritem}.txt")
    shell:
        "workflow/scatter --input {input} --output '{output}'"

# takes directory of outputs and processes each in parallel
rule third_rule:
    input:
        "intermediate/multiple_outputs/{scatteritem}.txt"
    output:
        "intermediate/processed_{scatteritem}.txt"
    shell:
        "workflow/parallel_processing_script --input {input} --output {output}"

# takes directory of outputs and processes each in parallel
rule fourth_rule:
    input:
        "intermediate/processed_{scatteritem}.txt"
    output:
        "intermediate/final_processed_{scatteritem}.txt"
    shell:
        "workflow/another_script --input {input} --output {output}"

# gathers the results
rule final_rule:
    input:
        gather.split("intermediate/final_processed_{scatteritem}.txt")
    output:
        "results/final_output.txt"
    shell:
        "workflow/aggregation_script --input_dir intermediate/ --output {output}"