Snakemake – A framework for reproducible data analysis(snakemake.github.io)

    with open('data/samples.txt') as slist:
        SAMPLES = [l.strip() for l in slist.readlines()]
    
    rule all:
        input:
            "results/line_counts.txt"
    
    rule count_lines:
        input:
            "data/lines/{sample}.txt"
        output:
            "processed/count_lines/{sample}.txt"
        shell:
            """
            cat {input} |
              wc -l | 
              paste <(echo -e {wildcards.sample}) - > {output}
            """
    
    rule collect_counts:
        input:
            expand("processed/count_lines/{sample}.txt", sample=SAMPLES)
        output:
            "results/line_counts.txt"
        shell:
            """
            cat <(echo -e "sample\tn_lines") {input} > {output}
            """