Johannes Köster

2020

 

https://koesterlab.github.io

Reproducible data analysis with

https://snakemake.readthedocs.io

dataset

results

Data analysis

"Let me do that by hand..."

https://snakemake.readthedocs.io

dataset

results

dataset

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dataset

"Let me do that by hand..."

Data analysis

https://snakemake.readthedocs.io

dataset

results

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automation

From raw data to final figures:

  • document parameters, tools, versions
  • execute without manual intervention

Reproducible data analysis

https://snakemake.readthedocs.io

dataset

results

dataset

dataset

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scalability

Handle parallelization:

  • execute for tens to thousands of datasets
  • efficiently use any computing platform

automation

Reproducible data analysis

https://snakemake.readthedocs.io

dataset

results

dataset

dataset

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Handle deployment:

be able to easily execute analyses on a different system/platform/infrastructure

portability

scalability

automation

Reproducible data analysis

https://snakemake.readthedocs.io

214k downloads since 2015

Snakemake is popular

611 citations (+359 in 2018 and 2019)

~3 citations per week

https://snakemake.readthedocs.io

dataset

results

dataset

dataset

dataset

dataset

dataset

scalability

automation

portability

https://snakemake.readthedocs.io

dataset

results

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dataset

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dataset

Define workflows

in terms of rules

https://snakemake.readthedocs.io

Define workflows

in terms of rules

https://snakemake.readthedocs.io

rule mytask:
    input:
        "path/to/{dataset}.txt"
    output:
        "result/{dataset}.txt"
    script:
        "scripts/myscript.R"


rule myfiltration:
     input:
        "result/{dataset}.txt"
     output:
        "result/{dataset}.filtered.txt"
     shell:
        "mycommand {input} > {output}"


rule aggregate:
    input:
        "results/dataset1.filtered.txt",
        "results/dataset2.filtered.txt"
    output:
        "plots/myplot.pdf"
    script:
        "scripts/myplot.R"

Define workflows

in terms of rules

https://snakemake.readthedocs.io

Define workflows

in terms of rules

rule mytask:
    input:
        "data/{sample}.txt"
    output:
        "result/{sample}.txt"
    shell:
        "some-tool {input} > {output}"

rule name

how to create output from input

define

  • input
  • output
  • log files
  • parameters
  • resources

https://snakemake.readthedocs.io

rule mytask:
    input:
        "path/to/{dataset}.txt"
    output:
        "result/{dataset}.txt"
    script:
        "scripts/myscript.R"


rule myfiltration:
     input:
        "result/{dataset}.txt"
     output:
        "result/{dataset}.filtered.txt"
     shell:
        "mycommand {input} > {output}"


rule aggregate:
    input:
        "results/dataset1.filtered.txt",
        "results/dataset2.filtered.txt"
    output:
        "plots/myplot.pdf"
    script:
        "scripts/myplot.R"

Define workflows

in terms of rules

https://snakemake.readthedocs.io

Boilerplate-free integration of scripts

rule mytask:
    input:
        "data/{sample}.txt"
    output:
        "result/{sample}.txt"
    script:
        "scripts/myscript.py"

reusable

Python/R/Julia scripts

https://snakemake.readthedocs.io

import pandas as pd

data = pd.read_table(snakemake.input[0])
data = data.sort_values("id")
data.to_csv(snakemake.output[0], sep="\t")

Python scripts:

Boilerplate-free integration of scripts

https://snakemake.readthedocs.io

Jupyter notebook integration

rule mytask:
    input:
        "data/{sample}.txt"
    output:
        "result/{sample}.txt"
    notebook:
        "notebooks/mynotebook.ipynb"
  1. Integrated interactive edit mode.
  2. Automatic generalization for reuse in other jobs.

https://snakemake.readthedocs.io

Reusable wrappers

rule map_reads:
    input:
        "{sample}.bam"
    output:
        "{sample}.sorted.bam"
    wrapper:
        "0.22.0/bio/samtools/sort"

reuseable wrappers from central repository

https://snakemake.readthedocs.io

Output handling

rule mytask:
    input:
        "data/{sample}.txt"
    output:
        temp("result/{sample}.txt")
    shell:
        "some-tool {input} > {output}"

https://snakemake.readthedocs.io

Output handling

rule mytask:
    input:
        "data/{sample}.txt"
    output:
        protected("result/{sample}.txt")
    shell:
        "some-tool {input} > {output}"

https://snakemake.readthedocs.io

Output handling

rule mytask:
    input:
        "data/{sample}.txt"
    output:
        pipe("result/{sample}.txt")
    shell:
        "some-tool {input} > {output}"

https://snakemake.readthedocs.io

dataset

results

dataset

dataset

dataset

dataset

dataset

scalability

automation

portability

https://snakemake.readthedocs.io

Scheduling

Paradigm:

Workflow definition shall be independent of computing platform and available resources

Rules:

define resource usage (threads, memory, ...)

Scheduler:

  • solves multidimensional knapsack problem
  • schedules independent jobs in parallel
  • passes resource requirements to any backend

https://snakemake.readthedocs.io

Scalable to any platform

workstation

compute server

cluster

grid computing

cloud computing

https://snakemake.readthedocs.io

Command-line interface

# perfom dry-run
snakemake -n

# execute workflow locally with 16 CPU cores
snakemake --cores 16


# execute on cluster
snakemake --cluster qsub --jobs 100


# execute in the cloud
snakemake --kubernetes --jobs 1000 --default-remote-provider GS --default-remote-prefix mybucket

https://snakemake.readthedocs.io

Between workflow caching

dataset

results

dataset

dataset

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dataset

dataset

shared data

https://snakemake.readthedocs.io

Between workflow caching

https://snakemake.readthedocs.io

dataset

results

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Full reproducibility:

install required software and all dependencies in exact versions

portability

scalability

automation

https://snakemake.readthedocs.io

rule mytask:
    input:
        "path/to/{dataset}.txt"
    output:
        "result/{dataset}.txt"
    conda:
        "envs/some-tool.yaml"
    shell:
        "some-tool {input} > {output}"

Conda integration

channels:
 - conda-forge
dependencies:
  - some-tool =2.3.1
  - some-lib =1.1.2

https://snakemake.readthedocs.io

Container integration

rule mytask:
    input:
        "path/to/{dataset}.txt"
    output:
        "result/{dataset}.txt"
    container:
        "docker://biocontainers/some-tool#2.3.1"
    shell:
        "some-tool {input} > {output}"

https://snakemake.readthedocs.io

Containers + Conda

container:
    "docker://continuumio/miniconda3:4.4.1"


rule mytask:
    input:
        "path/to/{dataset}.txt"
    output:
        "result/{dataset}.txt"
    conda:
        "envs/some-tool.yaml"
    shell:
        "some-tool {input} > {output}"

define OS

define tools/libs

https://snakemake.readthedocs.io

Self-contained HTML reports

https://snakemake.readthedocs.io

More features

  • conditional execution
  • graph partitioning
  • resource-constrained scheduling
  • various ways to constrain or enforce job execution
  • data provenance and log file handling
  • CWL integration
  • ...

https://snakemake.readthedocs.io

Conclusion

With

  • the human readable specification language
  • reusable modularization capabilities
  • seamless execution on all platforms without adaptation of the workflow definition
  • integrated package management and containerization

Snakemake covers all three dimensions of fully reproducible data analysis.

portability

scalability

automation

https://snakemake.readthedocs.io

Acknowledgements

Contributors:

Andreas Wilm

Anthony Underwood

Ryan Dale

David Alexander

Elias Kuthe

Elmar Pruesse

Hyeshik Chang

Jay Hesselberth

Jesper Foldager

John Huddleston

all users and supporters

Joona Lehtomäki

Justin Fear

Karel Brinda

Karl Gutwin

Kemal Eren

Kostis Anagnostopoulos

Kyle A. Beauchamp

Simon Ye

Tobias Marschall

Willem Ligtenberg

Development team:

Christopher Tomkins-Tinch

David Koppstein

Tim Booth

Manuel Holtgrewe

Christian Arnold

Wibowo Arindrarto

Rasmus Ågren

 

Kyle Meyer

Lance Parsons

Manuel Holtgrewe

Marcel Martin

Matthew Shirley

Mattias Franberg

Matt Shirley

Paul Moore

percyfal

Per Unneberg

 

Ryan C. Thompson

Ryan Dale

Sean Davis

https://snakemake.readthedocs.io

Reproducible data analysis with Snakemake (25min)

By Johannes Köster

Reproducible data analysis with Snakemake (25min)

Data analyses usually entail the application of many command line tools or scripts to transform, filter, aggregate or plot data and results. With ever increasing amounts of data being collected in science, reproducible and scalable automatic workflow management becomes increasingly important. Snakemake is a workflow management system, consisting of a text-based workflow specification language and a scalable execution environment, that allows the parallelized execution of workflows on workstations, compute servers, clusters and the cloud without modification of the workflow definition. Since its publication, Snakemake has been widely adopted and was used to build analysis workflows for a variety of high impact publications. With about thousands of homepage visits per month, it has a large and stable user community. This talk will show how Snakemake can be used to easily document, execute, and reproduce data analyses.

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