Johannes Köster

2019

 

https://koesterlab.github.io

Reproducible data analysis with

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results

Data analysis

"Let me do that by hand..."

dataset

results

dataset

dataset

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"Let me do that by hand..."

Data analysis

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results

dataset

dataset

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dataset

automation

From raw data to final figures:

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

Reproducible data analysis

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results

dataset

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dataset

dataset

dataset

scalability

Handle parallelization:

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

automation

Reproducible data analysis

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results

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dataset

dataset

Handle deployment:

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

portability

scalability

automation

Reproducible data analysis

100k downloads since 2015

50k in 2018

Snakemake is a popular solution

dataset

results

dataset

dataset

dataset

dataset

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scalability

automation

portability

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Define workflows

in terms of rules

Define workflows

in terms of rules

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

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
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

Define workflows

in terms of rules

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

reusable

Python/R scripts

External scripts

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:

External scripts

data <- read.table(snakemake@input[[1]])
data <- data[order(data$id),]
write.table(data, file = snakemake@output[[1]])

R scripts:

Define workflows

in terms of rules

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

reuseable wrappers from central repository

Define workflows

in terms of rules

use CWL tool

definitions

rule map_reads:
    input:
        "{sample}.bam"
    output:
        "{sample}.sorted.bam"
    cwl:
        "https://github.com/common-workflow-language/"
        "workflows/blob/fb406c95/tools/samtools-sort.cwl"

Output handling

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

Output handling

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

Output handling

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

dataset

results

dataset

dataset

dataset

dataset

dataset

scalability

automation

portability

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

Scalable to any platform

workstation

compute server

cluster

grid computing

cloud computing

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

Configuration profiles

snakemake --profile slurm --jobs 1000
$HOME/.config/snakemake/slurm
├── config.yaml
├── slurm-jobscript.sh
├── slurm-status.py
└── slurm-submit.py

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results

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Full reproducibility:

install required software and all dependencies in exact versions

portability

scalability

automation

Software installation is a pain

source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
easy_install snakemake
./configure --prefix=/usr/local
make
make install
cp lib/amd64/jli/*.so lib
cp lib/amd64/*.so lib
cp * $PREFIX
cpan -i bioperl
cmake ../../my_project \
    -DCMAKE_MODULE_PATH=~/devel/seqan/util/cmake \
    -DSEQAN_INCLUDE_PATH=~/devel/seqan/include
make
make install
apt-get install bwa
yum install python-h5py
install.packages("matrixpls")

Package management with

package:
  name: seqtk
  version: 1.2

source:
  fn: v1.2.tar.gz
  url: https://github.com/lh3/seqtk/archive/v1.2.tar.gz

requirements:
  build:
    - gcc
    - zlib
  run:
    - zlib

about:
  home: https://github.com/lh3/seqtk
  license: MIT License
  summary: Seqtk is a fast and lightweight tool for processing sequences

test:
  commands:
    - seqtk seq

Idea:

Normalization installation via recipes

#!/bin/bash

export C_INCLUDE_PATH=${PREFIX}/include
export LIBRARY_PATH=${PREFIX}/lib

make all
mkdir -p $PREFIX/bin
cp seqtk $PREFIX/bin
  • source or binary
  • recipe and build script
  • package
rule mytask:
    input:
        "path/to/{dataset}.txt"
    output:
        "result/{dataset}.txt"
    conda:
        "envs/some-tool.yaml"
    shell:
        "some-tool {input} > {output}"

Integration with Snakemake

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

Over 6000 bioinformatics related packages

Over 600 contributors

Singularity

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

Singularity + Conda

singularity:
    "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

Self-contained HTML reports

Sustainable publishing

# archive workflow (including Conda packages)
snakemake --archive myworkflow.tar.gz

Author:

  1.  
  2. Upload to Zenodo and acquire DOI.
  3. Cite DOI in paper.

Reader:

  1. Download and unpack workflow archive from DOI.
  2.  
# execute workflow (Conda packages are deployed automatically)
snakemake --use-conda --cores 16

More features

Today:

  • conditional DAG updates based on job output
  • semi-automatic graph partitioning
  • resource-constrained scheduling
  • various ways to constrain or enforce job execution
  • data provenance and log file handling
  • CWL export
  • ...

Future:

  • jupyter notebook integration
  • ML-based inference of resource requirements
  • more backends (TES, GCP)

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

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

Resources

Documentation and change log:

https://snakemake.readthedocs.io

 

Questions:

http://stackoverflow.com/questions/tagged/snakemake

 

Gold standard workflows:

https://github.com/snakemake-workflows/docs

 

Configuration profiles:

https://github.com/snakemake-profiles/doc

 

Command line help:

snakemake --help

Reproducible data analysis with Snakemake

By Johannes Köster

Reproducible data analysis with Snakemake

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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