Snakemake

In [ ]:

    

SAMPLES = ['ctl1', 'ctl2']

wdir = "/home/sergiu/data/work/course/short/data/snake/"

rule all:
    input:
        'merged.txt'

rule acounts:
    input:
        file='{sample}.fastq'
    output:
        '{sample}_counts.txt'
    run:
        with open(input.file, 'r') as f:
            nc = [str(l.count('A')) for l in f if not l[0]=='@']
        data = ', '.join(nc)+'\n'
        with open(output[0], 'w') as f: f.write(data)

rule merge:
    input:
        counts=expand('{sample}_counts.txt',sample=SAMPLES)
    output:
        'merged.txt'
    shell:
        """
        for f in {input.counts}
        do
			cat $f >> {output}
		done
        """


    

In [ ]:

    

snakemake --dag merged.txt | dot -Tsvg > dag.svg