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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

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nextflow implementation of the facets data flow.

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  • Nextflow 78.1%
  • R 14.2%
  • Dockerfile 7.7%