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phyloplace

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

https://github.com/nf-core/phyloplace

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.4%) to scientific vocabulary

Keywords

evolution evolutionary-tree nextflow nf-core phylogenetic-placement phylogenetics pipeline sequence-classification taxonomy-assignment workflow

Keywords from Contributors

metagenomics taxonomic-classification taxonomic-profiling
Last synced: 6 months ago · JSON representation ·

Repository

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

Basic Info
  • Host: GitHub
  • Owner: nf-core
  • License: mit
  • Language: Nextflow
  • Default Branch: master
  • Homepage: https://nf-co.re/phyloplace
  • Size: 3.43 MB
Statistics
  • Stars: 10
  • Watchers: 173
  • Forks: 5
  • Open Issues: 4
  • Releases: 2
Topics
evolution evolutionary-tree nextflow nf-core phylogenetic-placement phylogenetics pipeline sequence-classification taxonomy-assignment workflow
Created over 3 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/phyloplace

GitHub Actions CI Status GitHub Actions Linting StatusAWS CICite with Zenodo nf-test

Nextflow run with conda run with docker run with singularity Launch on Seqera Platform

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Introduction

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.

The pipeline is built using Nextflow, 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 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 in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the nf-core website.

Pipeline summary

  1. Optionally: Search a fasta file with a set of HMMER profiles. Best hits for each profile will be passed to the steps below.
  2. Align query sequences to the reference alignment using either HMMER, clustalo or MAFFT.
  3. Place query sequences in reference phylogeny with EPA-NG.
  4. Graft query sequences onto the reference phylogeny with GAPPA.
  5. If provided with a classification of the reference sequences, classify query sequences with GAPPA.

nf-core/phyloplace workflow overview

Usage

[!NOTE] If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

bash nextflow run nf-core/phyloplace \ -profile <docker/singularity/.../institute> \ --phyloplace_input samplesheet.csv \ --outdir <OUTDIR>

Or:

bash nextflow run nf-core/phyloplace \ -profile <docker/singularity/.../institute> \ --phylosearch_input search_params.csv \ --search_fasta sequences.faa \ --outdir <OUTDIR>

[!WARNING] Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/phyloplace was originally written by Daniel Lundin.

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

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #phyloplace channel (you can join with this invite).

Citations

If you use nf-core/phyloplace for your analysis, please cite it using the following doi: 10.5281/zenodo.7643941

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

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.

Owner

  • Name: nf-core
  • Login: nf-core
  • Kind: organization
  • Email: core@nf-co.re

A community effort to collect a curated set of analysis pipelines built using Nextflow.

Citation (CITATIONS.md) 

# nf-core/phyloplace: Citations

## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)

> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.

## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)

> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

## Pipeline tools

- [HMMER](https://pubmed.ncbi.nlm.nih.gov/22039361/)

  > Eddy, Sean R. “Accelerated Profile HMM Searches.” PLoS Comput Biol 7, no. 10 (October 20, 2011): e1002195. https://doi.org/10.1371/journal.pcbi.1002195.

- [Clustal Omega](https://pubmed.ncbi.nlm.nih.gov/21988835/)

  > Sievers, F., A. Wilm, D. Dineen, T. J. Gibson, K. Karplus, W. Li, R. Lopez, et al. 2011. “Fast, Scalable Generation of High-Quality Protein Multiple Sequence Alignments Using Clustal Omega.” Molecular Systems Biology 7 (1): 539–539. https://doi.org/10.1038/msb.2011.75.

- [MAFFT](https://pubmed.ncbi.nlm.nih.gov/12136088/)

  > Katoh, Kazutaka, Kazuharu Misawa, Kei‐ichi Kuma, and Takashi Miyata. “MAFFT: A Novel Method for Rapid Multiple Sequence Alignment Based on Fast Fourier Transform.” Nucleic Acids Research 30, no. 14 (July 15, 2002): 3059–66. https://doi.org/10.1093/nar/gkf436.

- [EPA-NG](https://pubmed.ncbi.nlm.nih.gov/30165689/)

  > Barbera, Pierre, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, and Alexandros Stamatakis. “EPA-Ng: Massively Parallel Evolutionary Placement of Genetic Sequences.” Systematic Biology 68, no. 2 (March 1, 2019): 365–69. https://doi.org/10.1093/sysbio/syy054.

- [Gappa](https://pubmed.ncbi.nlm.nih.gov/32016344/)

  > Czech, Lucas, Pierre Barbera, and Alexandros Stamatakis. “Genesis and Gappa: Processing, Analyzing and Visualizing Phylogenetic (Placement) Data.” Bioinformatics 36, no. 10 (May 1, 2020): 3263–65. https://doi.org/10.1093/bioinformatics/btaa070.

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)

  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.

- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)

  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.

- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)

  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.

- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.

- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

GitHub Events

Total
  • Create event: 6
  • Issues event: 3
  • Release event: 1
  • Watch event: 4
  • Issue comment event: 32
  • Push event: 16
  • Pull request review comment event: 40
  • Pull request review event: 40
  • Pull request event: 25
  • Fork event: 2
Last Year
  • Create event: 6
  • Issues event: 3
  • Release event: 1
  • Watch event: 4
  • Issue comment event: 32
  • Push event: 16
  • Pull request review comment event: 40
  • Pull request review event: 40
  • Pull request event: 25
  • Fork event: 2

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 91
  • Total Committers: 3
  • Avg Commits per committer: 30.333
  • Development Distribution Score (DDS): 0.044
Past Year
  • Commits: 81
  • Committers: 2
  • Avg Commits per committer: 40.5
  • Development Distribution Score (DDS): 0.012
Top Committers
Name Email Commits
Daniel Lundin e****l@g****m 87
Daniel Lundin m****s@g****m 3
James A. Fellows Yates j****3@g****m 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 4
  • Total pull requests: 20
  • Average time to close issues: about 2 months
  • Average time to close pull requests: 12 days
  • Total issue authors: 1
  • Total pull request authors: 3
  • Average comments per issue: 1.5
  • Average comments per pull request: 1.5
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 9
  • Average time to close issues: 12 minutes
  • Average time to close pull requests: 4 days
  • Issue authors: 1
  • Pull request authors: 3
  • Average comments per issue: 2.0
  • Average comments per pull request: 1.56
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • erikrikarddaniel (4)
Pull Request Authors
  • nf-core-bot (17)
  • erikrikarddaniel (15)
  • CaparicaLeo (1)
Top Labels
Issue Labels
enhancement (4)
Pull Request Labels

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • nf-core/tower-action v3 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • actions/checkout v2 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
.github/workflows/linting.yml actions
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/setup-python v4 composite
  • actions/upload-artifact v3 composite
  • mshick/add-pr-comment v1 composite
  • nf-core/setup-nextflow v1 composite
  • psf/black stable composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact v2 composite
  • marocchino/sticky-pull-request-comment v2 composite
modules/nf-core/custom/dumpsoftwareversions/meta.yml cpan
modules/nf-core/epang/place/meta.yml cpan
modules/nf-core/epang/split/meta.yml cpan
modules/nf-core/mafft/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
subworkflows/nf-core/fasta_newick_epang_gappa/meta.yml cpan
pyproject.toml pypi