mitopy-nf

Nextflow implementation of mitopy pipeline. Allows for running the pipeline efficiently on multiple samples.

How to run

Prerequisities

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

Input params

• --alignments Path to directory containing alignment files (BAM/CRAM format) and respective index files index files
• --mt-reference [rCRS|RSRS] (default: rCRS) Mitochondrial reference genome.
• --reference-fa Path to reference genome FASTA. Only required when alignments are in CRAM format. FASTA index and dictionary have to be in the same directory.
• --outdir (default: ./outputs) Output directory

Run pipeline on example data

Clone the repository

git clone https://github.com/bendda/mitopy-nf.git

Run the pipeline on subsampled BAM files of 3 samples from phase3 1000 Genomes Project:

cd mitopy-nf

nextflow run main.nf \
    --alignments 'example_data/*.{bam,bai}' \
    --outdir results

Run pipeline on your data

To run pipeline on your data, it is not necessary to clone the repository, pipeline can be easily run as follows:

# Help
nextflow run bendda/mitopy-nf -r main -latest --help

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

Run on DNAnexus

Import pipeline via CLI

$ dx build --nextflow \
  --repository https://github.com/bendda/mitopy-nf \
  --destination project-xxxx:/applets/mitopy-nf

Running a Nextflow Pipeline Applet via CLI

$ dx run project-xxxx:/applets/mitopy-nf \
  -ialignments="dx://project-xxxx:/inputs/*.{bam,bai}" \
  -ioutdir="dx://project-xxxx:/results/" \
  --brief -y

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