papaemmelab/nf-purple

Nextflow Pipeline to run Purple from HmfTools

🟣 nf-purple

Nextflow Pipeline to run Purple in Tumor-Only mode, uses Amber and Cobalt from HMFTools suite, of the Hartwig Foundation.

🚀 Run Pipeline

You need Nextflow installed.

module load java/jdk-11.0.11

nextflow papaemmelab/nf-purple \
    --tumor $tumor \
    --tumor_bam $TUMOR_BAM \
    --outdir $OUTDIR \
    ...refargs

🧬 Get Reference Data

Downloaded from Purple Ref Data for genome version 37. More information on their docs.

📒 Tools Info

Purple

Purple is a purity ploidy estimator for whole genome sequenced (WGS) data. It combines B-allele frequency (BAF) from AMBER, read depth ratios from COBALT, somatic variants and structural variants to estimate the purity and copy number profile of a tumor sample. PURPLE supports both grch 37 and 38 reference assemblies.

Amber

Amber is designed to generate a tumor BAF file for use in PURPLE from a provided VCF of likely heterozygous SNP sites.

Cobalt

Cobalt. Count bam lines determines the read depth ratios of the supplied tumor and reference genomes.

🕵🏻‍♂️ Tests

sh tests/run_test.sh

To check tests and update snapshots run:

nf-test test --update-snapshot

Docker

Purple Docker image was built for several platforms using docker buildx.

# Create a new builder instance
docker buildx create --name papaemmelab-builder --use

# Build the image
docker buildx build --platform linux/amd64,linux/arm64 -t papaemmelab/purple:v0.1.0 . --push