marielataretu / nextflow-mwe

Minimal, workable example of Nextflow

nextflow-mwe

Minimal, workable example of Nextflow

Requirements

• Unix-like operating system (Linux, macOS, etc)
• Java 11

Quickstart

1. Install Nextflow (version 23.04.0 or later):

    curl -s https://get.nextflow.io | bash
   

2. Launch the pipeline execution:

./nextflow run MarieLataretu/nextflow-mwe \
    -r v1.0 \
    -profile local,mamba

Components

This minimal examples uses the following software components and tools:

• fastp

Chen, Shifu. 2023. “ Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp.” iMeta 2, e107. https://doi.org/10.1002/imt2.107

• BWA

Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]