Changes between Version 2 and Version 3 of SOPs/nextflow


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Timestamp:
03/25/25 15:29:29 (10 days ago)
Author:
xinlei.gao
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  • SOPs/nextflow

    v2 v3  
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    22== What is Nextflow?
    3 Nextflow 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.
     3Nextflow is a workflow system for creating scalable, portable, and reproducible workflows. It has been developed specifically to ease the creation and execution of bioinformatics pipelines. 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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    1717This allows you to resume its execution, from the last successfully executed step, no matter what the reason was for it stopping.
    1818
    19 3. Portable
     193. Portability
    2020Nextflow can be executed on multiple platforms without changing its codes.
    2121
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    6060
    61 This is a simple script showing the basic 'Hello World!' example for the Nextflow framework. It will download a trivial example from the repository published at http://github.com/nextflow-io/hello and execute it on your computer.
     61This is a simple script showing the basic 'Hello World!' example for the Nextflow framework. It will download a trivial example from the repository published at http://github.com/nextflow-io/hello and execute it on your computer. Run this example to confirm all tools are installed properly.
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    6363
    6464== What is nf-core?
    6565
     66nf-core is a global community effort to collect a curated set of open‑source analysis pipelines built using Nextflow.
     67There are 128 pipelines that are currently available as part of nf-core. Browse them at https://nf-co.re/pipelines/.
     68== How to run nf-core pipelines
     69To run a pipeline:
    6670
    67 == The guidelines for running nf-core pipelines
     711. Choose a pipeline to run. See the available nf-core pipelines. If you have nf-core tools installed, run
     72{{{
     73nf-core pipelines list
     74}}}
    6875
    6976
     772. Configure Nextflow to run on your system:
    7078
     79The simplest way to run is with -profile docker (or singularity). This instructs Nextflow to execute jobs locally, with Docker (or Singularity) to fulfill software dependencies.
     80
     81Please note that if you are running the pipeline on the slurm cluster, you can only use -profile singularity, because you don't have the permission to run docker on it.
     82
     83Conda is also supported with -profile conda. However, this option is not recommended, as reproducibility of results can’t be guaranteed without containerization.
     84
     85
     863. Run the tests for your pipeline in the terminal to confirm everything is working:
     87
     88
     89{{{
     90nextflow run nf-core/<pipeline_name> -profile test,singularity --outdir <OUTDIR>
     91}}}
     92
     93Replace <pipeline_name> with the name of an nf-core pipeline.
     94
     95Nextflow will pull the code from the GitHub repository and fetch the software requirements automatically, so there is no need to download anything first.
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     97
     984. Read the pipeline documentation to see which command-line parameters are required. This will be specific to your data type and usage.
     99
     1005. To launch the pipeline with real data, omit the test config profile and provide the required pipeline-specific parameters. For example, to run the CUTandRun pipeline, your command will be similar to this:
     101
     102
     103{{{
     104nextflow run nf-core/cutandrun
     105-profile singularity
     106—input samplesheet.csv
     107—peakcaller ‘seacr,MACS2’
     108—genome GRCh38
     109—outdir nextflow_cutandrun
     110}}}
     111
     1126. Once complete, check the pipeline execution and quality control reports (such as multiqc_report.html files for MultiQC reports). Each pipeline’s documentation describes the outputs to expect.
     113
     114Please refer to nf-core documentation for more details (https://nf-co.re/docs/usage/getting_started/introduction).
    71115== Run nf-core pipelines on the slurm cluster
    72116