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sgnf

SocialGene's Nextflow Pipeline

https://github.com/socialgene/sgnf

Science Score: 44.0%

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
  • ✓
    DOI references
    Found 7 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.9%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

SocialGene's Nextflow Pipeline

Basic Info
Statistics
  • Stars: 1
  • Watchers: 2
  • Forks: 1
  • Open Issues: 10
  • Releases: 55
Created almost 4 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing Funding License Code of conduct Citation

README.md

Note: All releases may introduce breaking changes until the release of v1.0.0

Launch on Nextflow Tower

<!-- run with conda --> <!-- GitHub Actions CI Status GitHub Actions Linting Status -->

Documentation

Can be found at https://socialgene.github.io

Usage

Nextflow run with docker

:::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. :::

Note that this pipeline can initiate significant number of compute processes. If you are running on a cloud service you alone are responsible for any costs.

```bash outdir="pathtomy/outdir" outdirdownloadcache="pathtomy/outdirdownloadcache"

nextflow run socialgene/sgnf \ -profile ultraquickstart,docker \ --outdir $outdir \ --outdirdownloadcache $outdirdownloadcache ```

Unlike nf-core hosted pipelines, you should be able to use configuration files to run the pipeline. A number of examples are available https://github.com/socialgene/sgnf/tree/main/conf/examples

Credits

socialgene/sgnf was originally written by Chase M. Clark.

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

Contributions and Support

Chase M. Clark (and thus this project) was supported by an NLM training grant to the Computation and Informatics in Biology and Medicine Training Program (NLM 5T15LM007359)

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.

Docker Images

Docker image versions are synced via GitHub actions to be identical to the GitHub release version and the Nextflow pipeline version.

DockerPulls DockerImageSize(latestbydate) DockerImageVersion(latestsemver) DockerPulls

DockerPulls DockerImageSize(latestbydate) DockerImageVersion(latestsemver) DockerPulls

DockerPulls DockerImageSize(latestbydate) DockerImageVersion(latestsemver) DockerPulls

DockerPulls DockerImageSize(latestbydate) DockerImageVersion(latestsemver) DockerPulls

DockerPulls DockerImageSize(latestbydate) DockerImageVersion(latestsemver) DockerPulls

Skip Setup and Launch on...

This pipeline can be launched directly from Launch on Nextflow Tower or Run an example with Gitpod

Schema

image

Owner

  • Name: socialgene
  • Login: socialgene
  • Kind: organization

Citation (CITATIONS.md) 

# socialgene/sgnf: 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

- [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
  • Release event: 5
  • Delete event: 3
  • Issue comment event: 11
  • Push event: 20
  • Pull request event: 12
  • Create event: 8
Last Year
  • Release event: 5
  • Delete event: 3
  • Issue comment event: 11
  • Push event: 20
  • Pull request event: 12
  • Create event: 8

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment v1 composite
.github/workflows/ci.yml actions
  • actions/checkout v3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/cla.yml actions
  • contributor-assistant/github-action v2.3.0 composite
.github/workflows/clean-up.yml actions
  • actions/stale v7 composite
.github/workflows/docker.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
  • docker/login-action f4ef78c080cd8ba55a85445d5b36e214a81df20a composite
  • docker/metadata-action v4 composite
  • docker/setup-buildx-action v2 composite
  • docker/setup-qemu-action v2 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
  • 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_please.yml actions
  • google-github-actions/release-please-action v3 composite
dockerfiles/antismash/antismash-base/environment.yaml conda
  • antismash 6.1.1
  • procps-ng
  • python 3.10
dockerfiles/hmmer/environment.yaml conda
  • coreutils
  • gzip >=1.12
  • hmmer >=3.3.2
  • procps-ng
dockerfiles/hmmer_plus/environment.yaml conda
  • coreutils
  • curl
  • git
  • gzip >=1.12
  • hmmer >=3.3.2
  • procps-ng
  • unzip
  • wget
dockerfiles/sgpy/sgpy_base/environment.yaml conda
  • aspera-cli 3.9.6
  • bc >=1.07.1
  • biopython >=1.79
  • coreutils >=9.3
  • diamond 2.0.15
  • entrez-direct 16.2
  • git >=2.41
  • grep >=3.4
  • gzip >=1.12
  • hmmer 3.3.2
  • mmseqs2 13.45111
  • ncbi-datasets-cli 14.13.2
  • numpy >=1.24
  • openjdk >=17
  • pigz >=2.6
  • pip >=23.1.2
  • procps-ng >=4.0
  • python 3.10
  • rsync >=3.2.7
  • samtools 1.16.1
  • sed >=4.8
  • seqkit 2.3.0
  • tabix 1.11
  • wget >=1.20
  • zip >=3.0
dockerfiles/antismash/Dockerfile docker
  • chasemc2/antismash 6.1.1 build
dockerfiles/antismash/antismash-base/Dockerfile docker
  • mambaorg/micromamba 1.4.3 build
dockerfiles/hmmer/Dockerfile docker
  • mambaorg/micromamba 1.1.0 build
dockerfiles/hmmer_plus/Dockerfile docker
  • mambaorg/micromamba 1.1.0 build
dockerfiles/minimal/Dockerfile docker
  • python alpine3.17 build
dockerfiles/sgpy/Dockerfile docker
  • chasemc2/sgpy-base 1.0.1 build
dockerfiles/sgpy/sgpy_base/Dockerfile docker
  • mambaorg/micromamba 1.1.0 build