Dampier Lab Snakemake Wrappers

A collection of snakemake wrappers that are not suitable for the wider snakemake-wrappers config.

Usage

The wrappers are designed to be used in the snakemake workflow. They can be used from the Github repo directly.

rule dorado_duplex:
    input:
        "data/reads.fastq.gz"
    output:
        "data/reads.duplex.fastq.gz"
    wrapper:
        "https://github.com/damlab/damlab-wrappers/blob/main/dorado/duplex"

For certain tools, you may need to install the tool environment separately.

git clone https://github.com/damlab/damlab-wrappers.git
cd damlab-wrappers
make install

rule strainline_haplotypes:
    input:
        "data/reads.fastq.gz"
    output:
        "data/haplotypes.fasta"
    params:
        prefix = f"{wrappers_path}/strainline/venv"
    wrapper:
        f"file://{wrappers_path}/strainline/strainline"

Dorado basecalling

This package contains wrappers for the Nanopore dorado tool.

• dorado/duplex : Nanopore dorado duplex basecalling tool. Supports GPU acceleration and optional reference-based alignment.
• dorado/simplex : Nanopore dorado simplex basecalling tool. Supports GPU acceleration and optional reference-based alignment.
• dorado/demux : Nanopore dorado demultiplexing tool. Supports various barcoding kits and custom barcode arrangements.
• dorado/aligner : Nanopore dorado aligner tool. Supports GPU acceleration and optional reference-based alignment.

POD5

This package contains wrappers for the POD5 file format.

• pod5/convert_fast5 : Convert Oxford Nanopore FAST5 files to the newer POD5 format.
• pod5/split_by_channel : Split POD5 files by channel.

Multiple sequence alignment

This package contains wrappers for the multiple sequence alignment tools.

• MSA/muscle : MUSCLE multiple sequence alignment tool.

Strainline

This package contains wrappers for the Strainline reference free haplotype assembly tool. This package requires the strainline tool to be installed via the provided makefile.

• strainline/strainline : Strainline haplotype assembly tool.
• strainline/clipqs : ClipQS tool to orient and clip sequences generated by the Strainline tool.

Seqkit

This package contains wrappers that extend the Seqkit tool.

• seqkit/primercheck : Seqkit primer checking tool. Given a primer file and a set of reads, it will check if the reads contain the primers and return the amplicon length.

Cigarmath

This package contains wrappers for the Cigarmath library.

• cigarmath/deletion_frequency : Calculate the deletion frequency of a given region.

Phylogenetic tree construction

This package contains wrappers for the Phylogenetic tree construction tools.

• phylo/FastTree : Fasttree phylogenetic tree construction tool.
• phylo/phytreeviz : Phytreeviz tool for visualizing phylogenetic trees.
• phylo/reroot : Rerooting tool to reroot a tree using dendropy.

Barcode and UMI

This package contains wrappers for the barcode and UMI tools.

• barcode/extract : Extract barcodes and UMIs from a BAM file.
• barcode/correct : Correct barcodes in a BAM file.

Huggingface

This package contains wrappers for various AI tools.

• huggingface/hiv-bert : Run HIV-BERT models on provided sequences.

Visualization

A collection of snakemake wrappers of Python APIs for visualization.

• visualization/jaspar2logo : Create sequence logos from frequency counts.

Miscellaneous

• picard/addorreplacereadgroups : Picard tool to add or replace read groups in a BAM file. Slightly modified to have an easier way to set parameters.

Testing

Use make test to check all tests.