Data

Tools

Indexes

Applications

Experiments

Open Source Science

phageannotator

https://github.com/hofflab/phageannotator

Science Score: 26.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 10 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: HoffLab
  • License: mit
  • Language: Nextflow
  • Default Branch: dev
  • Size: 389 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 1
  • Open Issues: 1
  • Releases: 0
Created about 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

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

HoffLab/phageannotator is a bioinformatics pipeline that ...

  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.

Now, you can run the pipeline using:

bash nextflow run HoffLab/phageannotator \ -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

HoffLab/phageannotator was originally written by @CarsonJM.

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: HoffLab
  • Login: HoffLab
  • Kind: organization

GitHub Events

Total
Last Year

Dependencies

.github/workflows/branch.yml actions
  • mshick/add-pr-comment b8f338c590a895d50bcbfa6c5859251edc8952fc composite
.github/workflows/ci.yml actions
  • actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
  • jlumbroso/free-disk-space 54081f138730dfa15788a46383842cd2f914a1be composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/clean-up.yml actions
  • actions/stale 28ca1036281a5e5922ead5184a1bbf96e5fc984e composite
.github/workflows/download_pipeline.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • eWaterCycle/setup-singularity 931d4e31109e875b13309ae1d07c70ca8fbc8537 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/fix-linting.yml actions
  • actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • peter-evans/create-or-update-comment 71345be0265236311c031f5c7866368bd1eff043 composite
.github/workflows/linting.yml actions
  • actions/checkout b4ffde65f46336ab88eb53be808477a3936bae11 composite
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • actions/upload-artifact 5d5d22a31266ced268874388b861e4b58bb5c2f3 composite
  • nf-core/setup-nextflow v1 composite
.github/workflows/linting_comment.yml actions
  • dawidd6/action-download-artifact f6b0bace624032e30a85a8fd9c1a7f8f611f5737 composite
  • marocchino/sticky-pull-request-comment 331f8f5b4215f0445d3c07b4967662a32a2d3e31 composite
.github/workflows/release-announcements.yml actions
  • actions/setup-python 0a5c61591373683505ea898e09a3ea4f39ef2b9c composite
  • rzr/fediverse-action master composite
  • zentered/bluesky-post-action 80dbe0a7697de18c15ad22f4619919ceb5ccf597 composite