1. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101017529.
Copernicus - eoSC AnaLytics Engine
C-SCALE tutorial: Snakemake
Sebastian Luna-Valero, EGI Foundation
sebastian.luna.valero@egi.eu
C-SCALE tutorial: Snakemake | 29th November 2022 | Online

2. Outline
• Why workflows?
• Why snakemake?
• Let’s build a workflow!
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online

3. Why workflows?
Credits: https://github.com/c-scale-community/use-case-hisea
Goals:
● from raw data to figures
○ with “one click”
● re-run with new config
○ spatial scale
○ temporal scale
● re-run half-way through
○ recover from issues
● dependency management
○ between tasks
○ software packages
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online

4. Why workflows?
When to build a workflow?
● Re-run the same analysis over and over again, with different input parameters
● Ability to re-run the work partially; recover from intermediate failures
● Combine together heterogeneous tooling into the same analysis
○ Python, R, Julia, Docker, Bash, etc.
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online

5. Why snakemake?
• Mature workflow management system.
• Great community around it.
• Easy to learn? :)
• A Snakemake workflow scales without modification from single core workstations and
multi-core servers to batch systems (e.g. slurm)
• Snakemake integrates with the package manager Conda and the container engine
Singularity such that defining the software stack becomes part of the workflow itself.
• Further information: https://snakemake.readthedocs.io/
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online

6. Let’s build a workflow!
• Snakemake follows the GNU Make paradigm: workflows are defined in terms of rules that
define how to create output files from input files.
• $ snakemake --cores 1
• The application of a rule to generate a set of output files is called job.
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"european-countries.txt"
output:
"number-of-countries.txt"
shell:
"wc --lines european-countries.txt > number-of-countries.txt"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile

7. Let’s build a workflow!
• Snakemake follows the GNU Make paradigm: workflows are defined in terms of rules that
define how to create output files from input files.
• $ snakemake --cores 1
• Snakemake only re-runs jobs if one of the input files is newer than one of the output files
or one of the input files will be updated by another job.
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"european-countries.txt"
output:
"number-of-countries.txt"
shell:
"wc --lines european-countries.txt > number-of-countries.txt"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Belgium
Snakefile

8. Let’s build a workflow!
• Generalize the rule:
• $ snakemake --cores 1
• $ wc --lines european-countries.txt > number-of-countries.txt
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"european-countries.txt"
output:
"number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile

9. Let’s build a workflow!
• Adding more than one input file:
• $ snakemake --cores 1
• $ wc --lines european-countries.txt other-countries.txt
> number-of-countries.txt
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"european-countries.txt",
"other-countries.txt"
output:
"number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada

10. Let’s build a workflow!
• It’s better to organize your working directory:
• $ snakemake --cores 1
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada

11. Let’s build a workflow!
• Connecting rules! Targets can be rules, output files.
• $ snakemake --cores 1 <target>
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
shell:
"touch pre-processing.done"
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada

12. Let’s build a workflow!
• Updating intermediate files (however: #1978 and #2011)
• $ snakemake --cores 1 <target>
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
shell:
"touch pre-processing.done"
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
Snakefile $ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Belgium
$ cat other-countries.txt
US
Canada

13. Let’s build a workflow!
• Dependencies between the rules are determined creating a Directed Acyclic Graph
• $ snakemake --cores 1 --dag | dot -Tsvg > dag.svg
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
shell:
"touch pre-processing.done"
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
Snakefile

14. Let’s build a workflow!
• Python
• $ snakemake --cores 1 <target>
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
shell:
"python --input stats/number-of-countries.txt myscript.py"
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
Snakefile

15. Let’s build a workflow!
• Containers
• $ snakemake --cores 1 <target>
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
shell:
"udocker run example"
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
Snakefile

16. Let’s build a workflow!
• Pre-built support for Singularity (see docs for more details)
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
container:
"docker://repo/image"
script:
"scripts/plot.R"
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
Snakefile

17. Let’s build a workflow!
• Configuration
• $ snakemake --cores 1
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
configfile: "config.yaml"
rule count_countries:
input:
expand("{input}", input=config['european']),
expand("{input}", input=config['other'])
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile $ cat config.yaml
european: 'countries/european-countries.txt'
other: 'countries/other-countries.txt'
$ cat other-countries.txt
US
Canada

18. Let’s build a workflow!
• Logging
• $ snakemake --cores 1
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
log:
"logs/count_countries.log"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada

19. Let’s build a workflow!
• Benchmarking
• $ snakemake --cores 1
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
benchmark:
"benchmarks/count_countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada

20. Let’s build a workflow!
• Modularization
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada
include: "rules/count_countries.smk"
rule pre_processing:
input:
"stats/number-of-countries.txt"
output:
"pre-processing.done"
shell:
"touch pre-processing.done"
Snakefile

21. Let’s build a workflow!
• Integration with conda
• $ snakemake --cores 1 --use-conda --conda-frontend mamba
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"countries/european-countries.txt",
"countries/other-countries.txt"
output:
"stats/number-of-countries.txt"
conda:
"envs/count_countries.yaml"
shell:
"wc --lines {input} > {output}"
$ cat european-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
$ cat other-countries.txt
US
Canada
$ cat envs/count_countries.yaml
name: count_countries
channels:
- conda-forge
- defaults
dependencies:
- coreutils

22. Let’s build a workflow!
• Other examples
• https://github.com/c-scale-community/c-scale-tutorial-snakemake
• https://github.com/c-scale-community/use-case-hisea/pull/41/files
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online

23. Let’s build a workflow!
• Advanced features
• Pre-built functionality for scatter-gather jobs
• Cluster execution: snakemake --cluster qsub (see SLURM docs)
• Self-contained HTML reports
• Accessing remote storage:
• Amazon S3, Google Cloud Storage, Microsoft Azure Blob Storage
• SFTP, HTTP, FTP, Dropbox, XRootD, WebDAV, GFAL, GridFTP, iRODs, etc.
• Best practices
• https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html
• FAQs: https://snakemake.readthedocs.io/en/stable/project_info/faq.html
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online

24. Thank you for your attention.
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 101017529.
Copernicus - eoSC AnaLytics Engine
contact@c-scale.eu
https://c-scale.eu
@C_SCALE_EU
C-SCALE tutorial: Snakemake | 29th November 2022 | Online
Sebastian Luna-Valero, EGI Foundation
sebastian.luna.valero@egi.eu

25. Let’s build a workflow!
• Wildcards example:
• $ snakemake --cores 1 stats/number-of-european-countries.txt
• $ snakemake --cores 1 stats/number-of-other-countries.txt
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
rule count_countries:
input:
"countries/{category}-countries.txt"
output:
"stats/number-of-{category}-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat list-of-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile

26. Let’s build a workflow!
• Many to many with glob_wildcards:
• $ snakemake --cores 1
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online
CATEGORIES, = glob_wildcards("countries/{category}-countries.txt")
print(CATEGORIES)
rule all:
input:
expand("stats/number-of-{category}-countries.txt", category=CATEGORIES)
rule count_countries:
input:
"countries/{category}-countries.txt"
output:
"stats/number-of-{category}-countries.txt"
shell:
"wc --lines {input} > {output}"
$ cat list-of-countries.txt
Netherlands
Greece
Spain
Portugal
Italy
Poland
Austria
Snakefile
input-1
input-2
output-1
output-2
input-n output-n
input-.. output-..

27. Let’s build a workflow!
• Dependencies between the rules are determined automatically, creating a DAG (directed
acyclic graph) of jobs that can be automatically parallelized.
• Snakemake only re-runs jobs if one of the input files is newer than one of the output files
or one of the input files will be updated by another job.
• https://github.com/snakemake/snakemake/issues/1978
• Snakemake works backwards from requested output, and not from available input.
• Targets
• rule names can be targets
• output files can be targets
• if no target is given at the command line, Snakemake will define the first rule of the
Snakefile as the target. Hence, it is best practice to have a rule all at the top of the
workflow which has all typically desired target files as input files.
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C-SCALE tutorial: Snakemake | 29th November 2022 | Online