diff --git a/R/tso.R b/R/tso.R index 184418b..048e993 100644 --- a/R/tso.R +++ b/R/tso.R @@ -301,8 +301,8 @@ tso_tmbt_read <- function(x) { VariantType = "c", CosmicIDs = "c", MaxCosmicCount = "d", AlleleCountsGnomadExome = "d", AlleleCountsGnomadGenome = "d", AlleleCounts1000Genomes = "d", MaxDatabaseAlleleCounts = "d", - GermlineFilterDatabase = "l", GermlineFilterProxi = "l", - CodingVariant = "l", Nonsynonymous = "l", IncludedInTMBNumerator = "l" + GermlineFilterDatabase = "c", GermlineFilterProxi = "c", + CodingVariant = "c", Nonsynonymous = "c", IncludedInTMBNumerator = "c" ) # cttso v2 has introduced a few extra columns ct2 <- list( diff --git a/man/MultiqcFile.Rd b/man/MultiqcFile.Rd index fa35899..335d5bd 100644 --- a/man/MultiqcFile.Rd +++ b/man/MultiqcFile.Rd @@ -12,7 +12,8 @@ Contains methods for reading and displaying contents of the x <- "/path/to/multiqc_data.json" mqc <- MultiqcFile$new(x) mqc_parsed <- mqc$read() # or read(mqc) -mqc$write(mqc_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "tsv") +outdir <- "nogit" +mqc$write(mqc_parsed, out_dir = outdir, prefix = "SBJ02862_PRJ222112", out_format = "tsv") mqc_plots_parsed <- mqc$read(plot = TRUE, plot_names = "everything") mqc$write(mqc_plots_parsed, out_dir = tempdir(), prefix = "sample705", out_format = "rds") } diff --git a/tests/testthat/test-roxytest-testexamples-multiqc.R b/tests/testthat/test-roxytest-testexamples-multiqc.R index ef37638..a135344 100644 --- a/tests/testthat/test-roxytest-testexamples-multiqc.R +++ b/tests/testthat/test-roxytest-testexamples-multiqc.R @@ -2,7 +2,7 @@ # File R/multiqc.R: @testexamples -test_that("Function multiqc_date_fmt() @ L348", { +test_that("Function multiqc_date_fmt() @ L360", { cdate <- "2023-04-07, 09:09 UTC" (res1 <- multiqc_date_fmt(cdate))