Linux command
nextflow 命令
网络
复制后可按需替换文件名、目录或参数。
常用示例
Run pipeline
nextflow run [pipeline.nf]
Run with parameters
nextflow run [pipeline.nf] --input [data.txt]
Run pipeline from GitHub
nextflow run [user/repo]
Resume failed run from checkpoint
nextflow run [pipeline.nf] -resume
Run with Docker containers
nextflow run [pipeline.nf] -with-docker
Run with a specific config profile
nextflow run [pipeline.nf] -profile [docker]
Generate execution report and timeline
nextflow run [pipeline.nf] -with-report -with-timeline
Show pipeline info
nextflow info [pipeline]
List previous runs
nextflow log
Clean up cached work directories
nextflow clean -f
说明
nextflow is a reactive workflow framework and DSL for writing data-intensive computational pipelines. It enables the rapid composition of parallel and distributed pipelines using isolated processes connected by dataflow channels. Nextflow abstracts execution from pipeline logic, allowing the same workflow to run locally, on HPC clusters (SLURM, SGE, PBS, LSF), or on cloud platforms (AWS Batch, Azure Batch, Google Cloud, Kubernetes). It provides built-in support for containers (Docker, Singularity, Podman) and package managers (Conda), and uses content-addressable caching to enable safe resumption of failed runs.
参数
- run _PIPELINE_
- Execute a pipeline project (local path, script, or GitHub repo).
- pull _PROJECT_
- Download or update a remote project.
- info _PROJECT_
- Show system or pipeline info.
- log
- Show history of executions.
- clean
- Clean up work directories from past executions.
- drop _PROJECT_
- Delete a local project cache.
- list
- List downloaded pipeline projects.
- -resume _SESSION_
- Resume execution from cached results; optionally specify session ID.
- -with-docker _IMAGE_
- Enable Docker container execution.
- -with-podman _IMAGE_
- Enable Podman container execution.
- -with-singularity _IMAGE_
- Enable Singularity container execution.
- -with-conda _ENV_
- Enable Conda environment management.
- -profile _NAME_
- Select a configuration profile defined in nextflow.config.
- -c _FILE_, -config _FILE_
- Use an alternative configuration file.
- -params-file _FILE_
- Load pipeline parameters from JSON/YAML file.
- -w _DIR_, -work-dir _DIR_
- Directory for intermediate task files (default: ./work).
- -with-report _FILE_
- Generate an HTML execution report.
- -with-timeline _FILE_
- Generate a timeline HTML file.
- -with-trace _FILE_
- Generate an execution trace file.
- -with-dag _FILE_
- Generate a workflow DAG diagram.
- -bg
- Run in background.
- -r _REV_
- Use a specific Git revision/branch/tag.
- -h, -help
- Display help information.
FAQ
What is the nextflow command used for?
nextflow is a reactive workflow framework and DSL for writing data-intensive computational pipelines. It enables the rapid composition of parallel and distributed pipelines using isolated processes connected by dataflow channels. Nextflow abstracts execution from pipeline logic, allowing the same workflow to run locally, on HPC clusters (SLURM, SGE, PBS, LSF), or on cloud platforms (AWS Batch, Azure Batch, Google Cloud, Kubernetes). It provides built-in support for containers (Docker, Singularity, Podman) and package managers (Conda), and uses content-addressable caching to enable safe resumption of failed runs.
How do I run a basic nextflow example?
Run `nextflow run [pipeline.nf]` in a terminal, then adjust file names, paths, flags, or remote targets for your system.
What does run _PIPELINE_ do in nextflow?
Execute a pipeline project (local path, script, or GitHub repo).