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nextflow-base

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About

A basic boilerplate structure for Nextflow based pipelines with continues integration test case added. This is mostly inspired by nf-core code and structure style.

Currently on this pipeline three basic steps on any Sequence based analysis (starts from fastq files) present -

  • Quality Check (using fastqc)
  • Filtering (Using fastp)
  • Sequence Read Quantification (Using kallisto)

This can be used as a base to add other process.

Clone and Modify

git clone https://github.com/codingene/nextflow-base.git

Test Run

Without cloning if just want to test run it.

nextflow run codingene/nextflow-base -profile test,docker

This will directly pull the repo from GitHub and execute.

Check the Documentation for more.

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