Snakefile

# Note that if you are working on the analysis development locally, i.e. outside
# of the REANA platform, you can proceed as follows:
#
#   $ mkdir snakemake-local-run
#   $ cd snakemake-local-run
#   $ virtualenv ~/.virtualenvs/helloworld-snakemake
#   $ source ~/.virtualenvs/helloworld-snakemake/bin/activate
#   $ pip install snakemake
#   $ cp -a ../code ../data .
#   $ snakemake -s ../workflow/snakemake/Snakefile \
#               --configfile ../workflow/snakemake/inputs.yaml -p --cores 1
#   $ cat results/greetings.txt
#   Hello Jane Doe!
#   Hello Joe Bloggs!

rule all:
    input:
        "results/greetings.txt"

rule helloworld:
    input:
        helloworld=config["helloworld"],
        inputfile=config["inputfile"],
    params:
        sleeptime=config["sleeptime"]
    output:
        "results/greetings.txt"
    container:
        "docker://docker.io/library/python:2.7-slim"
    shell:
        "python {input.helloworld} "
        "--inputfile {input.inputfile} "
        "--outputfile {output} "
        "--sleeptime {params.sleeptime}"