Quick demo for Snakemake to present during the Hacky Hour at DPG spring meeting in Erlangen 2022.

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snakemake-demo
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Joint session AGI/AKjDPG
AGI 1.2: Talk
Wednesday, March 16, 2022, 14:45-15:15, AGI-H20
Link to proceedings: https://www.dpg-verhandlungen.de/year/2022/conference/erlangen/part/agi/session/1/contribution/2

Installation

Code Snippets

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import pandas as pd

locations = list()

for city_file in snakemake.input["tickets"]:
    with open (city_file, "r") as f:
        city_name = f.readline().strip()

        locations.append(city_name)

df = pd.DataFrame(locations, columns=["city"])
df.to_csv(snakemake.output["tickets"])
Python Pandas From line 1 of scripts/combine_tickets.py 
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with open(snakemake.input["city"], "r") as f:
    city_name = f.readline().strip()

with open(snakemake.output["city"], "w") as f:
    print(f"Hello {city_name}!", file=f)
Python From line 1 of scripts/greet_city.py 
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import pandas as pd

tickets = pd.read_csv(snakemake.input["tickets"])
conferences = pd.read_csv(snakemake.input["conferences"])

schedule = conferences[conferences["City"].isin(tickets["city"])]

schedule.to_csv(snakemake.output["schedule"])
Python Pandas From line 1 of scripts/make_conference_schedule.py 
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print("Hello World")
Python From line 1 of scripts/say_hello.py 
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script:
    "scripts/say_hello.py"
SnakeMake From line 2 of workflow/Snakefile 
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script:
    "scripts/greet_city.py"
SnakeMake From line 13 of workflow/Snakefile 
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script:
    "scripts/greet_city.py"
SnakeMake From line 21 of workflow/Snakefile 
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script:
    "scripts/greet_city.py"
SnakeMake From line 33 of workflow/Snakefile 
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script:
    "scripts/combine_tickets.py"
SnakeMake From line 46 of workflow/Snakefile 
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script:
    "scripts/make_conference_schedule.py"
SnakeMake From line 56 of workflow/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/euronion/snakemake-demo
Name: snakemake-demo
Version: 2
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Copyright: Public Domain
License: MIT License
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