CODEWITHSUNDEEP
snakemake
econ
econ

Reputation: 547

snakemake: write files from an array

I have an array xx = [1,2,3] and I want to use Snakemake to create a list of (empty) files 1.txt, 2.txt, 3.txt.

This is the Snakefile I use:

xx = [1,2,3]
rule makefiles:
    output: expand("{f}.txt", f=xx)
    run:
        with open(output, 'w') as file:
            file.write('blank')

However instead of having three new shiny text files in my folder I see an error message:

expected str, bytes or os.PathLike object, not OutputFiles

Not sure what I am doing wrong.

Upvotes: 1

Views: 214

Answers (1)

Manavalan Gajapathy
Manavalan Gajapathy

Reputation: 4089

Iterate output to get filenames and then write to them. See relevant documentation here.

rule makefiles:
    output: expand("{f}.txt", f=xx)
    run:
        for f in output:
            with open(f, 'w') as file:
                file.write('blank')

Rewriting above rule, to parallelize, by defining target files in rule all:

rule all:
    expand("{f}.txt", f=xx)

rule makefiles:
    output: 
        "{f}.txt"
    run:
        with open(output[0], 'w') as file:
           file.write('blank')

Upvotes: 1

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