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nf-seqsweep

https://github.com/xiaoli-dong/nf-seqsweep

Science Score: 39.0%

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
    Found .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 (13.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: xiaoli-dong
  • License: mit
  • Language: Nextflow
  • Default Branch: main
  • Size: 437 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

xiaoli-dong/seqsweep

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

xiaoli-dong/seqsweep is a bioinformatics pipeline that ... A nf-seqsweep analysis output demo page can be found at: https://xiaoli-dong.github.io/nf-seqsweep/ <!-- TODO nf-core: Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the major pipeline sections and the types of output it produces. You're giving an overview to someone new to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction -->

<!-- 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.

Now, you can run the pipeline using:

bash nextflow run xiaoli-dong/seqsweep \ -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

xiaoli-dong/seqsweep was originally written by Xiaoli Dong.

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: Xiaoli Dong
  • Login: xiaoli-dong
  • Kind: user
  • Location: Calgary
  • Company: Public Health Laboratory - South, Alberta Precision Laboratories

Bioinformatician

GitHub Events

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Last Year
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