Snakemake Dynamic Parallel Example

input.txt

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Snakefile

rule all:
    input: 'output.txt'

rule clean:
    shell: 'rm input_* intermediate_* output.txt'

rule merge:
    input: dynamic('intermediate_{n}.txt')
    output: 'output.txt'
    shell: 'cat {input} > {output}'

rule parallel:
    input: 'input_{n,\d+}.txt'
    output: 'intermediate_{n}.txt'
    shell: 'cat {input} > {output} && echo processed >> {output}'

rule split:
    input: 'input.txt'
    output: dynamic('input_{n}.txt')
    run:
        with open(input[0], 'r') as infile:
            for n, line in enumerate(infile.readlines()):
                with open('input_{}.txt'.format(n), 'w+') as outfile:
                    outfile.write(line)