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docs: fix stale 500K hypermutation threshold in cancer report QC table #104

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docs: fix stale 500K hypermutation threshold in cancer report QC table #104

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e494ed5
test: assert --dragen_hrd is optional in canrep CLI
qclayssen May 24, 2026
0c68a6f
docs: fix stale 500K hypermutation threshold in cancer report QC table
qclayssen Aug 4, 2026
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2 changes: 1 addition & 1 deletion inst/rmd/umccrise/cancer_report.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -407,7 +407,7 @@ qc_summary_all <- dplyr::tribble(
~n, ~variable, ~value, ~details,
4, "Hypermutated", ifelse(hypermutated, "TRUE", "FALSE"),
ifelse(hypermutated, glue::glue(
"More than 500K SNVs detected (including non-PASS), priority regions and/or variants ",
"More than 450K SNVs detected (including non-PASS), priority regions and/or variants ",
"selected for processing.",
), ""),
5, "MutSigs (Old)", glue::glue("{summarise_sigs(sigs_snv_2015)}"),
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51 changes: 51 additions & 0 deletions tests/testthat/test-canrep-cli.R
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@@ -0,0 +1,51 @@
# Tests for canrep CLI argument parsing
# Guards against regression where --dragen_hrd was accidentally marked required=TRUE
# (introduced in 563f946, fixed in PR #94 and again in 2.3.1)

canrep_parser <- function() {
cli_path <- system.file("cli/canrep.R", package = "gpgr")
source(cli_path, local = TRUE)
p <- argparse::ArgumentParser()
sp <- p$add_subparsers(dest = "command")
canrep_add_args(sp)
p
}

required_args <- function() {
c(
"canrep",
"--af_global", "x",
"--af_keygenes", "x",
"--batch_name", "x",
"--img_dir", "x",
"--key_genes", "x",
"--oncokb_genes", "x",
"--somatic_snv_vcf", "x",
"--somatic_snv_summary", "x",
"--somatic_sv_tsv", "x",
"--somatic_sv_vcf", "x",
"--purple_som_gene_cnv", "x",
"--purple_som_cnv_ann", "x",
"--purple_som_cnv", "x",
"--purple_purity", "x",
"--purple_qc", "x",
"--purple_som_snv_vcf", "x",
"--virusbreakend_tsv", "x",
"--virusbreakend_vcf", "x",
"--bcftools_stats", "x",
"--result_outdir", "x",
"--tumor_name", "x"
)
}

test_that("canrep parses without --dragen_hrd (optional)", {
p <- canrep_parser()
args <- p$parse_args(required_args())
expect_null(args$dragen_hrd)
})

test_that("canrep parses with --dragen_hrd when provided", {
p <- canrep_parser()
args <- p$parse_args(c(required_args(), "--dragen_hrd", "sample.hrdscore.csv"))
expect_equal(args$dragen_hrd, "sample.hrdscore.csv")
})