Nextflow implementation

Source code:: https://github.com/bendda/mitopy-nf

To run the mitopy pipeline at scale on multiple samples, we provide a Nextflow-based implementation of the pipeline, which can be seamlessly deployed to cloud-based environments or computing clusters.

By this implementation, we also demonstrate usage of mitopy as an underlying library for implementation of scalable pipelines in the workflow manager of choice.

How to run

Prerequisities

To run the pipeline, please install Nextflow and Docker on your system.

Input parameters

Parameter	Default	Description
`--alignments`	null	Path to directory containing alignment files (`.bam`) and respective index files (`.bai`). Ex: `path/to/bams/*.{bam,bai}`
`--mt-reference`	rCRS	Mitochondrial reference genome to use for analysis. By default, rCRS reference is used. RSRS reference is included as optional reference.
`--outdir`	./outputs	Output directory

Run pipeline

Run the pipeline on your data using following command (adjust alignments path):

# Run on bam alignment files located in TEST/ directory
nextflow run bendda/mitopy-nf -r main -latest \
    --alignments 'TEST/*.{bam,bai}' \
    --outdir results

Outputs

outputs/
├── alignments
│   ├── sample.bam
│   ├── sample.bam.bai
│   ├── sample_shifted.bam
│   ├── sample_shifted.bam.bai
├── annotation
│   ├── sample_annotated.csv
│   ├── sample_annotated.vcf
├── haplogroup_report
│   ├── sample_haplogroup.txt
├── variant_calls
│   ├── sample.vcf
│   ├── sample.vcf.idx
└── visualization
    ├── sample.html