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https://github.com/adamrtalbot/nf-demo

https://github.com/adamrtalbot/nf-demo

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
    Found .zenodo.json file
  • ○
    DOI references
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    Academic publication links
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: adamrtalbot
  • Language: R
  • Default Branch: main
  • Size: 344 KB
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  • Watchers: 1
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Created about 1 year ago · Last pushed about 1 year ago

https://github.com/adamrtalbot/nf-demo/blob/main/ 

# nf-demo

A Nextflow pipeline for demonstrating the value of Nextflow to R users.

## Overview

This pipeline has three variations on 3 branches:

1. `bash`: An R script manually called via a `bash` script
2. `nextflow`: A Nextflow pipeline
3. `platform`: A Nextflow pipeline configured with additional features to make it fully compatible with Seqera Platform

This pipeline processes RNA-Seq count data, performs quality control, and generates visualizations including PCA plots, count distributions, and sample correlations but this is not it's primary purpose.

## Requirements

- Nextflow
- Conda or Docker or Singularity

OR:

- R with packages:
  - ggplot2
  - jsonlite
- MultiQC

## Usage
Run the pipeline with:

```bash
nextflow run adamrtalbot/nf-demo --input 'path/to/*.csv' --output_dir results
```

## Input

The pipeline expects CSV files with the following input:

```csv
,Sample1,Sample2,Sample3,Sample4,Sample5,Sample6
ENSG00000000001,1,1,0,1,0,0
ENSG00000000002,558,1568,445,513,374,781
```

## Output

The pipeline generates a MultiQC document.

Owner

  • Name: Adam Talbot
  • Login: adamrtalbot
  • Kind: user
  • Location: Warwick, UK
  • Company: @seqeralabs

Bioinformatics Engineer at @seqeralabs

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