SPHN Workflow Interoperability Workshop
Johannes Köster
2018
https://koesterlab.github.io
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Data analysis
"Let me do that by hand..."
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"Let me do that by hand..."
Data analysis
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automation
From raw data to final figures:
- document parameters, tools, versions
- execute without manual intervention
Reproducible data analysis
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scalability
Handle parallelization:
- execute for tens to thousands of datasets
- efficiently use any computing platform
automation
Reproducible data analysis
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Handle deployment:
be able to easily execute analyses on a different system/platform/infrastructure
portability
scalability
automation
Reproducible data analysis
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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
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
Define workflows
in terms of rules
rule mytask:
input:
"data/{sample}.txt"
output:
"result/{sample}.txt"
script:
"scripts/myscript.py"
reusable
Python/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"
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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
# 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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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/mycommand.yaml"
shell:
"mycommand {input} > {output}"
Integration with Snakemake
channels:
- conda-forge
- defaults
dependencies:
- mycommand ==2.3.1
Over 3000 bioinformatics related packages
Over 200 contributors
Singularity
rule mytask:
input:
"path/to/{dataset}.txt"
output:
"result/{dataset}.txt"
singularity:
"docker://biocontainers/mycommand#2.3.1"
shell:
"mycommand {input} > {output}"
Singularity + Conda
singularity:
"docker://continuumio/miniconda3:4.4.1"
rule mytask:
input:
"path/to/{dataset}.txt"
output:
"result/{dataset}.txt"
conda:
"envs/mycommand.yaml"
shell:
"mycommand {input} > {output}"
define OS
define tools/libs
Sustainable publishing
# archive workflow (including Conda packages)
snakemake --archive myworkflow.tar.gz
Author:
- Upload to Zenodo and acquire DOI.
- Cite DOI in paper.
Reader:
- Download and unpack workflow archive from DOI.
# execute workflow (Conda packages are deployed automatically)
snakemake --use-conda --cores 16
Conclusion
With
- the rule-based DSL
- modularization via wrappers and CWL integration
- 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
Snakemake
By Johannes Köster
Snakemake
SPHN Workflow Interoperability Workshop
- 1,769