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

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CUT&RUN-Flow, A Nextflow pipeline for QC, tag trimming, normalization, and peak calling for data from CUT&RUN experiments.

README.rst

***********************
CUT&RUN-Flow (CnR-flow)
***********************
.. 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

Owner

Citation (Citations.bib)

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