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https://github.com/cdcgov/mycosnp-nf

CDCgov/mycosnp-nf
https://github.com/cdcgov/mycosnp-nf

myco nextflow nf-core snp

Last synced: 2 months ago
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CDCgov/mycosnp-nf

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README 

        
# ![CDCgov/mycosnp-nf](docs/images/nf-core-mycosnp_logo_light.png#gh-light-mode-only) ![CDCgov/mycosnp-nf](docs/images/nf-core-mycosnp_logo_dark.png#gh-dark-mode-only)



[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)

[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)

[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)



## Introduction



**nf-core/mycosnp** is a bioinformatics best-practice analysis pipeline for MycoSNP is a portable workflow for performing whole genome sequencing analysis of fungal organisms, including Candida auris. This method prepares the reference, performs quality control, and calls variants using a reference. MycoSNP generates several output files that are compatible with downstream analytic tools, such as those for used for phylogenetic tree-building and gene variant annotations..



The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!



## Pipeline summary



### Reference Preparation



> **Prepares a reference FASTA file for BWA alignment and GATK variant calling by masking repeats in the reference and generating the BWA index.**

* Genome repeat identification and masking (`nucmer`)

* BWA index generation (`bwa`)

* FAI and DICT file creation (`Picard`, `Samtools`)



### Sample QC and Processing



> **Prepares samples (paired-end FASTQ files) for GATK variant calling by aligning the samples to a BWA reference index and ensuring that the BAM files are correctly formatted. This step also provides different quality reports for sample evaluation.**



* Combine FASTQ file lanes if they were provided with multiple lanes.

* Filter unpaired reads from FASTQ files (`SeqKit`).

* Down sample FASTQ files to a desired coverage or sampling rate (`SeqTK`).

* Trim reads and assess quality (`FaQCs`).

* Generate a QC report by extracting data from FaQCs report data.

* Align FASTQ reads to a reference (`BWA`).

* Sort BAM files (`SAMTools`).

* Mark and remove duplicates in the BAM file (`Picard`).

* Clean the BAM file (`Picard "CleanSam"`).

* Fix mate information in the BAM file (`Picard "FixMateInformation"`).

* Add read groups to the BAM file (`Picard "AddOrReplaceReadGroups"`).

* Index the BAM file (`SAMTools`).

* [FastQC](#fastqc) - Filtered reads QC.

* Qualimap mapping quality report.

* [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline



### Variant calling and analysis



> **Calls variants and generates a multi-FASTA file and phylogeny.**



* Call variants (`GATK HaplotypeCaller`).

* Combine gVCF files from the HaplotypeCaller into a single VCF (`GATK CombineGVCFs`).

* Call genotypes using the (`GATK GenotypeGVCFs`).

* Filter the variants (`GATK VariantFiltration`) [default (but customizable) filter: 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || DP < 10'].

* Run a customized VCF filtering script (`Broad Institute`).

* Split the filtered VCF file by sample.

* Select only SNPs from the VCF files (`GATK SelectVariants`).

* Split the VCF file with SNPs by sample.

* Create a multi-fasta file from the VCF SNP positions using a custom script (`Broad`).

* Create a distance matrix file using multi-fasta file(`SNPdists`).

* Create phylogeny from multi-fasta file (`rapidNJ`, `FastTree2`, `quicksnp`, `RaxML(optional)`, `IQTree(optional)`)



### Variant annotation analysis (currently available for *C. auris* B11205 genome only)



* annotated VCF file (`snpEff`)

* combined output report(`SnpEffR`)



## Quick Start



1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)



2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_

3. Requires Python version >3.0



4. Download the pipeline and test it on a minimal dataset with a single command:



    ```console

    nextflow run CDCgov/mycosnp-nf -profile test,YOURPROFILE

    ```



    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.



    > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.

    > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.

    > * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.

    > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.



5. Start running your own analysis!



    ```console

    nextflow run CDCgov/mycosnp-nf -profile  --input samplesheet.csv --fasta c_auris.fasta

    ```

6. It is advisable to delete large temporary or log files after the successful completion of the run. It takes a lot of space and may cause issues in future runs.



## Pre-configured Nextflow development environment using Gitpod



>[![Open CDCgov/mycosnp-nf in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/CDCgov/mycosnp-nf)

>>Once the pod launches, it will present a VS-Code interface and comes with Nextflow, Conda and Docker pre-installed

## Documentation



The nf-core/mycosnp pipeline comes with documentation about the pipeline [usage](https://github.com/CDCgov/mycosnp-nf/blob/master/docs/usage.md), [parameters](https://github.com/CDCgov/mycosnp-nf/wiki/Parameter-Docs) and [output](https://github.com/CDCgov/mycosnp-nf/blob/master/docs/output.md).



## Credits



nf-core/mycosnp was originally written by CDC.



We thank the following people for their extensive assistance in the development of this pipeline:



* Michael Cipriano [@mjcipriano](https://github.com/mjcipriano)

* Sateesh Peri [@sateeshperi](https://github.com/sateeshperi)

* Hunter Seabolt [@hseabolt](https://github.com/hseabolt)

* Chris Sandlin [@cssandlin](https://github.com/cssandlin)

* Drewry Morris [@drewry](https://github.com/drewry)

* Lynn Dotrang [@leuthrasp](https://github.com/LeuThrAsp)

* Christopher Jossart [@cjjossart](https://github.com/cjjossart)

* Robert A. Petit III [@rpetit3](https://github.com/rpetit3)



> Special thanks the **Staph-B** Slack workspace for open-source collaborations and discussions.

## Contributions and Support



If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).



## Citations



An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.



You can cite the `MycoSNP` and `nf-core` publications as follows:



> Bagal UR, Phan J, Welsh RM, Misas E, Wagner D, Gade L, Litvintseva AP, Cuomo CA, Chow NA. 

> 

> MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris. 

> 

> _Methods Mol Biol._ 2022; 2517:215-228. doi: [10.1007/978-1-0716-2417-3_17](https://pubmed.ncbi.nlm.nih.gov/35674957)



> **The nf-core framework for community-curated bioinformatics pipelines.**

>

> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

>

> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).



# CDCgov GitHub Organization Open Source Project Template



**Template for clearance: This project serves as a template to aid projects in starting up and moving through clearance procedures. To start, create a new repository and implement the required [open practices](open_practices.md), train on and agree to adhere to the organization's [rules of behavior](rules_of_behavior.md), and [send a request through the create repo form](https://forms.office.com/Pages/ResponsePage.aspx?id=aQjnnNtg_USr6NJ2cHf8j44WSiOI6uNOvdWse4I-C2NUNk43NzMwODJTRzA4NFpCUk1RRU83RTFNVi4u) using language from this template as a Guide.**



**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm).  GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise. 



## Related documents



* [Open Practices](open_practices.md)

* [Rules of Behavior](rules_of_behavior.md)

* [Thanks and Acknowledgements](thanks.md)

* [Disclaimer](DISCLAIMER.md)

* [Contribution Notice](CONTRIBUTING.md)

* [Code of Conduct](code-of-conduct.md)

  

## Public Domain Standard Notice

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subject to domestic copyright protection under 17 USC § 105. This repository is in

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All contributions to this repository will be released under the CC0 dedication. By

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## License Standard Notice

The repository utilizes code licensed under the terms of the Apache Software

License and therefore is licensed under ASL v2 or later.



This source code in this repository is free: you can redistribute it and/or modify it under

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The source code forked from other open source projects will inherit its license.



## Privacy Standard Notice

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information. All material and community participation is covered by the

[Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)

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For more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).



## Contributing Standard Notice

Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)

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## Records Management Standard Notice

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## Additional Standard Notices

Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)

for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),

[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),

and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).