Data

Tools

Indexes

Applications

Experiments

Open Source Science

elucidatornf

A collection of workflows to stream together tools from within elucidator

https://github.com/nickjhathaway/elucidatornf

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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

A collection of workflows to stream together tools from within elucidator

Basic Info
  • Host: GitHub
  • Owner: nickjhathaway
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 181 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

nickjhathaway/elucidatornf

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo nf-test

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

Introduction

nickjhathaway/elucidatornf is a bioinformatics pipeline that ...

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 nickjhathaway/elucidatornf \ -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.

Credits

nickjhathaway/elucidatornf was originally written by Nicholas Hathaway.

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.

Citations

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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: Nicholas Hathaway
  • Login: nickjhathaway
  • Kind: user

I help to develop bioinformatics tools for infectious disease research with a primary focus on malaria sequencing analysis

Citation (CITATIONS.md) 

# nickjhathaway/elucidatornf: 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





## 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
  • Push event: 37
  • Create event: 3
Last Year
  • Push event: 37
  • Create event: 3

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 1
  • Total Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nicholas Hathaway n****y@g****m 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
.github/workflows/ci.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • conda-incubator/setup-miniconda a4260408e20b96e80095f42ff7f1a15b27dd94ca composite
  • eWaterCycle/setup-apptainer main composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/clean-up.yml actions
  • actions/stale 28ca1036281a5e5922ead5184a1bbf96e5fc984e composite
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • eWaterCycle/setup-apptainer 4bb22c52d4f63406c49e94c804632975787312b3 composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v2 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • peter-evans/create-or-update-comment 71345be0265236311c031f5c7866368bd1eff043 composite
.github/workflows/linting.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • actions/setup-python 82c7e631bb3cdc910f68e0081d67478d79c6982d composite
  • actions/upload-artifact 65462800fd760344b1a7b4382951275a0abb4808 composite
  • nf-core/setup-nextflow v2 composite
  • pietrobolcato/action-read-yaml 1.1.0 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 composite
  • marocchino/sticky-pull-request-comment 331f8f5b4215f0445d3c07b4967662a32a2d3e31 composite
.github/workflows/template_version_comment.yml actions
  • actions/checkout 0ad4b8fadaa221de15dcec353f45205ec38ea70b composite
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
  • nichmor/minimal-read-yaml v0.0.2 composite
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