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)}"), 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") +})