cancer_rmd: Generate UMCCR Cancer Report
In umccr/gpgr: Genomics Platform Group Reporting

cancer_rmd

R Documentation

Generate UMCCR Cancer Report

Description

Generates a UMCCR Cancer Report. It does so with the following steps:

move the img_dir into 'tmp/img_dir'
copy the rmd into 'tmp/cancer_report.Rmd'
render the rmd inside 'tmp/'
return the path to the output HTML

Usage

cancer_rmd(
  af_global,
  af_keygenes,
  batch_name,
  conda_list,
  dragen_hrd,
  img_dir,
  key_genes,
  oncokb_genes,
  virusbreakend_tsv,
  virusbreakend_vcf,
  purple_purity,
  purple_qc,
  purple_som_cnv_ann,
  purple_som_cnv,
  purple_som_gene_cnv,
  purple_som_snv_vcf,
  somatic_snv_vcf,
  somatic_snv_summary,
  somatic_sv_tsv,
  somatic_sv_vcf,
  result_outdir,
  tumor_name,
  out_file = NULL,
  quiet = FALSE
)

Arguments

`af_global`	Path to `af_tumor.txt` file.
`af_keygenes`	Path to `af_tumor_keygenes.txt` file.
`batch_name`	Name of batch sample.
`conda_list`	Path to `conda_pkg_list.txt` file.
`img_dir`	Path to directory containing PURPLE plots.
`key_genes`	Path to UMCCR cancer gene file.
`oncokb_genes`	Path to OncoKB database file.
`virusbreakend_tsv`	Path to VIRUSBreakend summary file.
`virusbreakend_vcf`	Path to VIRUSBreakend VCF file.
`purple_purity`	Path to `purple.purity.tsv`.
`purple_qc`	Path to `purple.qc`.
`purple_som_cnv_ann`	Path to annotated and prioritised `purple.cnv.somatic.tsv`.
`purple_som_cnv`	Path to `purple.cnv.somatic.tsv`.
`purple_som_gene_cnv`	Path to `purple.cnv.gene.tsv`.
`purple_som_snv_vcf`	Path to `purple.somatic.vcf.gz`.
`somatic_snv_vcf`	Path to `somatic-PASS.vcf.gz` SNV VCF.
`somatic_snv_summary`	Path to `somatic_snv_summary.json` JSON.
`somatic_sv_tsv`	Path to `manta.tsv` TSV file.
`somatic_sv_vcf`	Path to `manta.vcf.gz` VCF file.
`result_outdir`	Path to directory to write tidy JSON/TSV results.
`tumor_name`	Name of tumor sample.
`out_file`	Path to output HTML file (needs '.html' suffix) (def: `⁠{tumor_name}_cancer_report.html⁠`).
`quiet`	Suppress log printing during rendering.