From e494ed57f978bd5d0bf6ecc4538a8e04954f1a11 Mon Sep 17 00:00:00 2001
From: Quentin Clayssen <quentin.clayssen@gmail.com>
Date: Mon, 25 May 2026 09:55:42 +1000
Subject: [PATCH 1/2] test: assert --dragen_hrd is optional in canrep CLI

Regression guard: 563f946 accidentally re-introduced required=TRUE,
causing crashes on samples without DRAGEN HRD files.
---
 tests/testthat/test-canrep-cli.R | 51 ++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)
 create mode 100644 tests/testthat/test-canrep-cli.R

diff --git a/tests/testthat/test-canrep-cli.R b/tests/testthat/test-canrep-cli.R
new file mode 100644
index 0000000..d29caf7
--- /dev/null
+++ b/tests/testthat/test-canrep-cli.R
@@ -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")
+})

From 0c68a6f87a925e50894e3a902e8b39107b8d53c6 Mon Sep 17 00:00:00 2001
From: Quentin Clayssen <quentin.clayssen@gmail.com>
Date: Wed, 5 Aug 2026 09:31:16 +1000
Subject: [PATCH 2/2] docs: fix stale 500K hypermutation threshold in cancer
 report QC table

Actual bolt safety threshold is 450,000 (MAX_SOMATIC_VARIANTS, ADR-001),
not 500K.
---
 inst/rmd/umccrise/cancer_report.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/rmd/umccrise/cancer_report.Rmd b/inst/rmd/umccrise/cancer_report.Rmd
index d6be0a4..f720a31 100644
--- a/inst/rmd/umccrise/cancer_report.Rmd
+++ b/inst/rmd/umccrise/cancer_report.Rmd
@@ -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)}"),