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nf-core-ameta

An nf-core compliant version of aMeta; An ancient metagenomic profiling Snakemake workflow

https://github.com/nbisweden/nf-core-ameta

Science Score: 57.0%

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

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    CITATION.cff file
    Found CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 20 DOI reference(s) in README
  • ○
    Academic publication links
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.1%) to scientific vocabulary
Last synced: 9 months ago · JSON representation ·

Repository

An nf-core compliant version of aMeta; An ancient metagenomic profiling Snakemake workflow

Basic Info
  • Host: GitHub
  • Owner: NBISweden
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Size: 5.59 MB
Statistics
  • Stars: 2
  • Watchers: 5
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

README.md

nf-core/ameta

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

Get help on SlackFollow on TwitterFollow on MastodonWatch on YouTube

Introduction

nf-core/ameta is a bioinformatics pipeline that is a conversion of the ancient microbiome analysis workflow written in Snakemake: https://github.com/NBISweden/aMeta.

<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)

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.

[!IMPORTANT] Prebuilt databases are available from:

  • KrakenUniq DB on full NCBI NT: https://doi.org/10.17044/scilifelab.20205504
  • KrakenUniq DB on microbial part of NCBI NT: https://doi.org/10.17044/scilifelab.20518251
  • KrakenUniq DB on microbial part of NCBI RefSeq: https://doi.org/10.17044/scilifelab.21299541
  • Bowtie2 index for full NCBI NT database: https://doi.org/10.17044/scilifelab.21070063
  • Bowtie2 index on pathogenic microbes of NCBI NT: https://doi.org/10.17044/scilifelab.21185887

Now, you can run the pipeline using:

bash nextflow run nf-core/ameta \ -profile <docker/singularity/.../institute> \ --input samplesheet.csv \ --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/ameta was originally written by @mahesh-panchal.

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 #ameta channel (you can join with this invite).

Citations

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: NBIS - National Bioinformatics Infrastructure Sweden
  • Login: NBISweden
  • Kind: organization
  • Location: Sweden

NBIS is a distributed national bioinformatics infrastructure, supporting life sciences in Sweden.

Citation (CITATIONS.md) 

# nf-core/ameta: 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

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].

- [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

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Last Year
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  • Pull request review comment event: 3
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Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 7
  • Average time to close issues: 5 months
  • Average time to close pull requests: 2 months
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.33
  • Average comments per pull request: 1.14
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 5
  • Average time to close issues: 5 months
  • Average time to close pull requests: 3 months
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.33
  • Average comments per pull request: 1.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ZoePochon (2)
Pull Request Authors
  • mahesh-panchal (12)
Top Labels
Issue Labels
enhancement (1) bug (1)
Pull Request Labels

Dependencies

.github/workflows/awsfulltest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/awstest.yml actions
  • actions/upload-artifact v3 composite
  • seqeralabs/action-tower-launch v2 composite
.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v4 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout v4 composite
  • actions/setup-node v4 composite
.github/workflows/linting.yml actions
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  • 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
.github/workflows/release-announcements.yml actions
  • actions/setup-python v4 composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action v0.0.2 composite
modules/nf-core/bowtie2/align/meta.yml cpan
modules/nf-core/bowtie2/build/meta.yml cpan
modules/nf-core/cutadapt/meta.yml cpan
modules/nf-core/fastqc/meta.yml cpan
modules/nf-core/krakenuniq/build/meta.yml cpan
modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml cpan
modules/nf-core/krona/ktimporttaxonomy/meta.yml cpan
modules/nf-core/krona/ktupdatetaxonomy/meta.yml cpan
modules/nf-core/malt/build/meta.yml cpan
modules/nf-core/malt/run/meta.yml cpan
modules/nf-core/maltextract/meta.yml cpan
modules/nf-core/mapdamage2/meta.yml cpan
modules/nf-core/multiqc/meta.yml cpan
modules/nf-core/samtools/faidx/meta.yml cpan
modules/nf-core/samtools/flagstat/meta.yml cpan
modules/nf-core/samtools/idxstats/meta.yml cpan
modules/nf-core/samtools/index/meta.yml cpan
modules/nf-core/samtools/sort/meta.yml cpan
modules/nf-core/samtools/stats/meta.yml cpan
modules/nf-core/samtools/view/meta.yml cpan
subworkflows/nf-core/bam_sort_stats_samtools/meta.yml cpan
subworkflows/nf-core/bam_stats_samtools/meta.yml cpan
subworkflows/nf-core/fastq_align_bowtie2/meta.yml cpan
.github/workflows/download_pipeline.yml actions
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  • eWaterCycle/setup-apptainer 4bb22c52d4f63406c49e94c804632975787312b3 composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/template_version_comment.yml actions
  • actions/checkout 11bd71901bbe5b1630ceea73d27597364c9af683 composite
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  • nichmor/minimal-read-yaml v0.0.2 composite
modules/nf-core/bowtie2/align/environment.yml conda
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  • pigz 2.6.*
  • samtools 1.18.*
modules/nf-core/bowtie2/build/environment.yml conda
  • bowtie2 2.5.2.*
modules/nf-core/cutadapt/environment.yml conda
  • cutadapt 4.6.*
modules/nf-core/fastqc/environment.yml conda
  • fastqc 0.12.1.*
modules/nf-core/krakenuniq/build/environment.yml conda
  • krakenuniq 1.0.4.*
modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml conda
  • krakenuniq 1.0.4.*
modules/nf-core/krona/ktimporttaxonomy/environment.yml conda
  • krona 2.8.*
modules/nf-core/krona/ktupdatetaxonomy/environment.yml conda
  • krona 2.7.1.*
modules/nf-core/malt/build/environment.yml conda
  • malt 0.62.*
modules/nf-core/malt/run/environment.yml conda
  • malt 0.62.*
modules/nf-core/maltextract/environment.yml conda
  • hops 0.35.*
modules/nf-core/mapdamage2/environment.yml conda
  • mapdamage2 2.2.1.*
modules/nf-core/multiqc/environment.yml conda
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modules/nf-core/samtools/faidx/environment.yml conda
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modules/nf-core/samtools/flagstat/environment.yml conda
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  • samtools 1.21.*
modules/nf-core/samtools/idxstats/environment.yml conda
  • htslib 1.21.*
  • samtools 1.21.*
modules/nf-core/samtools/index/environment.yml conda
  • htslib 1.19.1.*
  • samtools 1.19.2.*
modules/nf-core/samtools/sort/environment.yml conda
  • htslib 1.19.1.*
  • samtools 1.19.2.*
modules/nf-core/samtools/stats/environment.yml conda
  • htslib 1.21.*
  • samtools 1.21.*
modules/nf-core/samtools/view/environment.yml conda
  • htslib 1.19.1.*
  • samtools 1.19.2.*
subworkflows/nf-core/utils_nextflow_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfcore_pipeline/meta.yml cpan
subworkflows/nf-core/utils_nfschema_plugin/meta.yml cpan
subworkflows/nf-core/utils_nfvalidation_plugin/meta.yml cpan