https://github.com/ssi-dk/calc-script-demux_illumina

https://github.com/ssi-dk/calc-script-demux_illumina

Last synced: 3 days ago
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• Host: GitHub
• URL: https://github.com/ssi-dk/calc-script-demux_illumina
• Owner: ssi-dk
• Created: 2022-07-28T08:52:13.000Z (over 2 years ago)
• Default Branch: master
• Last Pushed: 2022-07-29T12:56:02.000Z (over 2 years ago)
• Last Synced: 2023-03-02T02:46:28.835Z (over 1 year ago)
• Language: Jupyter Notebook
• Size: 8.79 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# calc-script-demux_illumina

A jupyter notebook wrapper related to finding new runs with different patterns in two folders.

## Requirements

- conda

## Installation

install conda env, recommendation is into project dir

`conda env create -p ./.venv --file ./notebooks/conda.env.yml`

Set the jupyter server to use the conda env

install conda env, recommendation is into project dir by pointing it to`./.venv`

Add associate input and output folders. The default location is `./input` and `./output`,

## Running

To run the notebook form CLI

`papermill ./notebooks/demux_illumina.ipynb -`

This will dump the output to stdout and stderr. Alternatively you can run and define a new notebook which will store associated outputs there.

See notebook for further details.