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https://github.com/rennelab/cnr-flow

CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.
https://github.com/rennelab/cnr-flow

chip-seq-pipelines cutandrun cutandrun-seq cutrun genomics nextflow peak-calling

Last synced: 4 months ago
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CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

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README 

        

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CUT&RUN-Flow (CnR-flow)

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.. image:: https://img.shields.io/github/v/release/rennelab/cnr-flow?include_prereleases&logo=github

   :target: https://github.com/rennelab/cnr-flow/releases

   :alt: GitHub release (latest by date including pre-releases)

.. image:: https://circleci.com/gh/RenneLab/CnR-flow.svg?style=shield&circle-token=0c2e0d49a95709cbb3f0bb8b7d8d05ffa4547d14

   :target: https://app.circleci.com/pipelines/github/RenneLab/CnR-flow

   :alt: CircleCI Build Status

.. image:: https://img.shields.io/readthedocs/cnr-flow?logo=read-the-docs

   :target: https://CnR-flow.readthedocs.io/en/latest/?badge=latest

   :alt: ReadTheDocs Documentation Status

.. image:: https://img.shields.io/badge/nextflow-%3E%3D20.10.6-green

   :target: https://www.nextflow.io/

   :alt: Nextflow Version Required >= 20.10.6

.. image:: https://img.shields.io/badge/License-GPLv3+-blue?logo=GNU

   :target: https://www.gnu.org/licenses/gpl-3.0.en.html

   :alt: GNU GPLv3+ License

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.4015698.svg

   :target: https://doi.org/10.5281/zenodo.4015698

   :alt: Zenodo DOI:10.5281/zenodo.4015698



| Welcome to *CUT&RUN-Flow* (*CnR-flow*), a Nextflow pipeline for QC, tag 

  trimming, normalization, and peak calling for paired-end sequencing 

  data from CUT&RUN experiments.

| This software is available via GitHub, at 

  http://www.github.com/RenneLab/CnR-flow .

| Full project documentation is available at |docs_link|_.



Pipeline Design:

    | CUT&RUN-Flow is built using `Nextflow`_, a powerful 

      domain-specific workflow language built to create flexible and 

      efficient bioinformatics pipelines. 

      Nextflow provides extensive flexibility in utilizing cluster 

      computing environments such as `PBS`_ and `SLURM`_, 

      and in automated and compartmentalized handling of dependencies using 

      `Conda`_ / `Bioconda`_, `Docker`_, `Singularity`_ or `Environment Modules`_.

    

Dependencies:

    | In addition to local configurations, Nextflow handles 

      dependencies in separated working environments within the same pipeline 

      using `Conda`_ or `Environment Modules`_ within your working environment,

      or using container-encapsulated execution with `Docker`_ or `Singularity`_. 

      **CnR-flow is pre-configured to auto-acquire dependencies with no additional setup,

      either using Conda recipes from the Bioconda project, 

      or by using Docker or Singularity to execute Docker images hosted by the

      BioContainers project** (`Bioconda`_; `BioContainers`_).



    | CUT&RUN-Flow utilizes 

      `UCSC Genome Browser Tools`_ and  `Samtools`_

      for reference library preparation,

      `FastQC`_ for tag quality control,

      `Trimmomatic`_ for tag trimming, `Bowtie2`_ for tag alignment,

      `Samtools`_, `bedtools`_ and `UCSC Genome Browser Tools`_

      for alignment manipulation, and `MACS2`_ and/or `SEACR`_

      for peak calling, as well as their associated language subdependencies of

      Java, Python2/3, R, and C++.



Pipeline Features:

    * One-step reference database prepration using a path (or URL)

      to a FASTA file.

    * Ability to specify groups

      of samples containing both treatment (Ex: H3K4me3) and 

      control (Ex: IgG) antibody

      groups, with automated association of each control sample with the 

      respective treatment samples during the peak calling step

    * Built-in normalization

      protocol to normalize to a sequence library of the user's choice

      when spike-in DNA is used in the CUT&RUN Protocol (Optional, includes an 

      *E. coli* reference genome for utiliziation of *E. coli* 

      as a spike-in control as described by |Meers2019| 

      [see the |References| section of |docs_link|_])

    * OR: CPM-normalization to normalize total read counts between samples (beta).

    * SLURM, PBS... and many other job scheduling environments 

      enabled natively by Nextflow

    * Output of memory-efficient CRAM (alignment), 

      bedgraph (genome coverage), 

      and bigWig (genome coverage) file formats



    |pipe_dotgraph|



| For a full list of required dependencies and tested versions, see 

  the |Dependencies| section of |docs_link|_, and for dependency 

  configuration options see the |Dependency Config| section.



.. _Quickstart:



Quickstart

------------

    Here is a brief introduction on how to install and get started using the pipeline. 

    For full details, see |docs_link|_.

    

    Prepare Task Directory:

        | Create a task directory, and navigate to it.

    

        .. code-block:: bash   

    

                $ mkdir ./my_task  # (Example)

                $ cd ./my_task     # (Example)

    

    Install Nextflow (if necessary):

        | Download the nextflow executable to your current directory.

        | (You can move the nextflow executable and add to $PATH for 

          future usage)

    

        .. code-block:: bash

    

            $ curl -s https://get.nextflow.io | bash

    

            # For the following steps, use:

            nextflow    # If nextflow executable on $PATH (assumed)

            ./nextflow  # If running nextflow executable from local directory

    

    Download and Install CnR-flow:

        | Nextflow will download and store the pipeline in the 

          user's Nextflow info directory (Default: ``~/.nextflow/``)

    

        .. code-block:: bash

    

            $ nextflow run RenneLab/CnR-flow --mode initiate    

    

    Configure, Validate, and Test:

        Conda: 

          * Install miniconda (if necessary).

            `Installation instructions `_

          * The CnR-flow configuration with Conda should then work "out-of-the-box."



        Docker:

          * Add '-profile docker' to all nextflow commands



        Singularity:

          * Add '-profile singularity' to all nextflow commands



        | If using an alternative configuration, see the |Dependency Config|

          section of |docs_link|_ for dependency configuration options.

        |

        | Once dependencies have been configured, validate all dependencies:

    

        .. code-block:: bash



            # Conda or other configs:    

            $ nextflow run CnR-flow --mode validate_all



            # OR Docker Configuration:    

            $ nextflow run CnR-flow -profile docker --mode validate_all



            # OR Singularity Configuration:    

            $ nextflow run CnR-flow -profile singularity --mode validate_all

    

        | Fill the required task input parameters in "nextflow.config"

          For detailed setup instructions, see the  |Task Setup| 

          section of |docs_link|_

          *Additionally, for usage on a SLURM, PBS, or other cluster systems, 

          configure your system executor, time, and memory settings.*

    

        .. code-block:: bash

    

            # Configure:

            $  nextflow.config   # Task Input, Steps, etc. Configuration

        

            #REQUIRED values to enter (all others *should* work as default):

            # ref_fasta               (or some other ref-mode/location)

            # treat_fastqs            (input paired-end fastq[.gz] file paths)

            #   [OR fastq_groups]     (mutli-group input paired-end .fastq[.gz] file paths)

    

    Prepare and Execute Pipeline:

        | Prepare your reference databse (and normalization reference) from .fasta[.gz]

          file(s): 

    

        .. code-block:: bash

    

            $ nextflow run CnR-flow --mode prep_fasta

    

        | Perform a test run to check inputs, paramater setup, and process execution:

    

        .. code-block:: bash

    

            $ nextflow run CnR-flow --mode dry_run

    

        | If satisifed with the pipeline setup, execute the pipeline:

    

        .. code-block:: bash

    

            $ nextflow run CnR-flow --mode run

    

        | Further documentation on CUT&RUN-Flow components, setup, and usage can

          be found in |docs_link|_.

    

.. |References| replace:: *References*

.. |Meers2019| replace:: *Meers et. al. (eLife 2019)*

.. |Dependency Config| replace:: *Dependency Configuration*

.. |Dependencies| replace:: *Dependencies*

.. |Task Setup| replace:: *Task Setup*

.. |pipe_dotgraph| image:: build_info/dotgraph_parsed.png

    :alt: CUT&RUN-Flow Pipe Flowchart

.. |docs_link| replace:: CUT&RUN-Flow's ReadTheDocs

.. _docs_link: https://cnr-flow.readthedocs.io#



.. _Nextflow: http://www.nextflow.io

.. _Bioconda: https://bioconda.github.io/

.. _CUTRUNTools: https://bitbucket.org/qzhudfci/cutruntools/src

.. _SEACR: https://github.com/FredHutch/SEACR

.. _R: https://www.r-project.org/

.. _Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

.. _faCount: https://hgdownload.cse.ucsc.edu/admin/exe/

.. _Samtools: http://www.htslib.org/

.. _FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

.. _Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic

.. _bedtools: https://bedtools.readthedocs.io/en/latest/

.. _bedGraphToBigWig: https://hgdownload.cse.ucsc.edu/admin/exe/

.. _MACS2: https://github.com/macs3-project/MACS

.. _PBS: https://www.openpbs.org/

.. _SLURM: https://slurm.schedmd.com/

.. _CONDA: https://anaconda.org/

.. _Environment Modules: http://modules.sourceforge.net/

.. _Docker: http://www.docker.com/

.. _Singularity: https://sylabs.io/

.. _BioContainers: https://biocontainers.pro/

.. _UCSC Genome Browser Tools: https://hgdownload.cse.ucsc.edu/admin/exe/

.. _kseq_test: https://bitbucket.org/qzhudfci/cutruntools/src

.. _CUT&RUN-Tools: https://bitbucket.org/qzhudfci/cutruntools/src