Nextflow Pipeline to run Purple in Tumor-Only mode, uses Amber and Cobalt from HMFTools suite, of the Hartwig Foundation.
You need Nextflow installed.
module load java/jdk-11.0.11
nextflow papaemmelab/nf-purple \
--tumor $tumor \
--tumor_bam $TUMOR_BAM \
--outdir $OUTDIR \
...refargsDownloaded from Purple Ref Data for genome version 37. More information on their docs.
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 is designed to generate a tumor BAF file for use in PURPLE from a provided VCF of likely heterozygous SNP sites.
Cobalt. Count bam lines determines the read depth ratios of the supplied tumor and reference genomes.
sh tests/run_test.shTo check tests and update snapshots run:
nf-test test --update-snapshotPurple 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