facets-nf

nextflow implementation of the facets data flow.

usage

For vcf, see the docs over at:

https://github.com/mskcc/facets/tree/master/inst/extcode

nextflow run brwnj/facets-nf -r v1.0.0 -profile docker \
    --vcf common_all.vcf.gz \
    --normal normal.recal.bam \
    --tumor tumor.recal.bam

results

The workflow runs snp-pileup and generates:

• facets.cncf
• facets.pdf
• facets.rdata