nextflow basics

Nextflow core knowledge points and usage guide

one,Installation and dependency

1. Environmental Requirements
   • Java: Nextflow requires a Java 17+ environment, which can be passedapt-getorSDKMANInstall.

   • Operating system: Supports Linux and macOS, and Windows needs to run through WSL2.

2. Installation method
   • One-click installation:

   curl -s  | bash
   chmod +x nextflow
   mv nextflow $HOME/.local/bin/
   

   Support automatic update (nextflow self-update）。
   • Conda installation:

   conda install -c bioconda nextflow
   

   Suitable for scenarios where version management is required.

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two,Core functions and advantages

1. Scalability
   • Supports on-premises, cluster (Slurm/SGE/PBS) and cloud platform (AWS/GCP) deployment.

   • Automatic parallelization: byChannelImplement task distribution without manually configuring parallel logic.

2. Containerization support
   • Seamless integration of Docker and Singularity to ensure environmental consistency.

   • Example:

   process samtools {
     container "biocontainers/samtools:1.3.1"
     script "samtools --version"
   }
   

3. Fault Tolerance and Recovery
   • Checkpoint mechanism: Can be passed after the task fails-resumeThe parameters continue from the breakpoint.

   • Automatic error log tracking, supporting dynamic resource adjustment.

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three,Script Development and Syntax

1. Process structure
   • Process: Defines a single task, including input, output, and script logic.

   process splitLetters {
     input: val str
     output: path 'chunk_*'
     script: "printf '$str' | split -b 6 - chunk_"
   }
   

   • Workflow: ByChannelConnect multiple Processes to define data flow.

2. Parameterization and configuration
   • Global parameters: PassparamsDefinition, support command line override.

    = "Hello world!"
   

   • Resource configuration:Specify CPU, memory, etc.

   process {
     executor = 'slurm'
     cpus = 8
     memory = '32 GB'
   }
   

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Four,Cloud Platform Integration (Taking AWS as an example)

1. Docking plan
   • The configuration file specifies cloud resource type, authentication information, and storage (such as S3).

   • Example:

   aws {
     region = 'us-east-1'
     accessKey = 'YOUR_KEY'
     secretKey = 'YOUR_SECRET'
   }
   

2. Optimization practice
   • Spot example: In combination with MemVerge MMCloud, low-cost fault tolerance (failure rate <1%).

   • Dynamic resource adjustment: Automatically select the optimal instance type through WaveRider.

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five,Debugging and best practices

1. Logs and monitoring
   • use-logThe parameters output detailed logs, combined with Nextflow Tower to visualize the process status.

   • Real-time monitoring of resource utilization (CPU/memory/storage).

2. Frequently Asked Questions
   • Permissions issue: AvoidrootRun, use Singularity instead of Docker.

   • Timeout processing:processSettings intimeParameters limit the task duration.

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Summarize
• Applicable scenarios: bioinformatics (such as gene sequencing), machine learning assembly line, large-scale data processing.

• Recommended configuration: Conda for local development, production environment prioritizes cloud clustering + containerization.

• Learning Resources: Official Documents (), nf-core community process template.

For complete parameter list or cloud deployment details, please refer toNextflow official documentationOr MemVerge's cloud optimization solution.