Changes between Initial Version and Version 1 of SOPs/nextflow


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Timestamp:
03/25/25 14:46:38 (9 months ago)
Author:
xinlei.gao
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  • SOPs/nextflow

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     2== What is Nextflow?
     3Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It allows you to run your analysis pipeline on a large-scale dataset in a streamlined and parallel manner. Nextflow can deploy workflows on a variety of execution platforms, including your local machine, HPC schedulers, and cloud. Additionally, Nextflow supports a range of compute environments, software container runtimes, and package managers, allowing workflows to be executed in reproducible and isolated environments.
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     6== Why using Nextflow?
     7The rise of big data has made it increasingly necessary to be able to analyze and perform experiments on large datasets in a portable and reproducible manner. Nextflow has several highlighted features that could be helpful in reproducible and efficient pipeline implementation.
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     91. Reproducibility
     10Nextflow supports Docker and Singularity containers technology.
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     12This, along with the integration of the GitHub code sharing platform, allows you to write self-contained pipelines, manage versions and to rapidly reproduce any former configuration.
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     142. Continuous checkpoints
     15All the intermediate results produced during the pipeline execution are automatically tracked.
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     17This allows you to resume its execution, from the last successfully executed step, no matter what the reason was for it stopping.
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     193. Portable
     20Nextflow can be executed on multiple platforms without changing its codes.
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     22It supports various executors including batch schedulers like SLURM, LSF, PBS, and cloud platforms, such as Kubernetes, Amazon AWS, Google Cloud and Microsoft Azure platforms.
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     25== Installation of Nextflow
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     29== What is nf-core?
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     32== The guidelines for running nf-core pipelines
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     36== Run nf-core pipelines on the slurm cluster
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     39== The recommendations of running individual nf-core pipelines
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     411. nf-core CUTandRun pipeline
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     432. nf-core Ribo-seq pipeline
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     453. nf-core ATAC-seq pipeline
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