The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.

GNU make와 유사한 파이프라인 프레임워크. Python 문법을 확장하여 구성됨.

팁 #

명령어 사용방법 #

스크립트에 문제가 없나 테스트

$ snakemake -n

전체 프로세스를 DAG로 가시화

$ snakemake --forceall --dag | dot -Tpdf > dag.pdf

10개의 job을 동시에 수행 (개별 rule에 threads 변수가 있는 경우, 그만큼 점유)

$ snakemake --cores 10

관련정보 #

• Snakemake Tutorial 2017
• PyCon Korea 2015: 탐색적으로 큰 데이터 분석하기 장혜식 at PyCon Korea 2015 2015-08-31

Incoming Links #

Related Medical Scholarly Articles (MedicalScholarlyArticle 0) #

• VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
• hppRNA-a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples

Codes Written (Code 1) #

• VIPER

Related Articles (Article 2) #

• Pipeline for Bioinformatics
• Tuxedo protocol

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