Generate UMCCR Cancer Report — cancer

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,
  bcftools_stats,
  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.
bcftools_stats: Path to bcftools_stats.txt file.
conda_list: Path to conda_pkg_list.txt file.
dragen_hrd: Path to DRAGEN hrdscore.csv 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 SV TSV file.
somatic_sv_vcf: Path to SV 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.

Value

Path to rendered HTML report.