Merge branch 'main' into oncoanalyser-sash-inputs

NAMESPACE

@@ -10,27 +10,6 @@ export(dragen_hrd)
 export(get_oncokb_genes)
 export(hrd_results_tabs)
 export(is_vcf)
-export(linx_breakend_process)
-export(linx_breakend_read)
-export(linx_clusters_process)
-export(linx_clusters_read)
-export(linx_drivercatalog_process)
-export(linx_drivercatalog_read)
-export(linx_drivers_process)
-export(linx_drivers_read)
-export(linx_fusion_process)
-export(linx_fusion_read)
-export(linx_links_process)
-export(linx_links_read)
-export(linx_rmd)
-export(linx_svs_process)
-export(linx_svs_read)
-export(linx_viscopynumber_read)
-export(linx_visfusion_read)
-export(linx_visgeneexon_read)
-export(linx_visproteindomain_read)
-export(linx_vissegments_read)
-export(linx_vissvdata_read)
 export(mkdir)
 export(pkg_exists)
 export(plot_bnd_sr_pr_tot_hist)

R/rmd.R

@@ -1,58 +1,3 @@
-#' Generate UMCCR LINX Report
-#'
-#' Generates a UMCCR LINX HTML report. It does so with the following steps:
-#' 1. recursively copy the table and plot directories into tmp/plot and tmp/table
-#' 2. copy the rmd into tmp/linx.Rmd
-#' 3. render the rmd inside tmp/
-#' 4. return the path to the output HTML
-#'
-#' @param sample Name of sample.
-#' @param table_dir Path to LINX table directory.
-#' @param plot_dir Path to LINX plot directory.
-#' @param out_file Path to output HTML file (needs '.html' suffix).
-#' @param quiet Suppress printing during rendering.
-#'
-#' @return Path to rendered HTML report.
-#' @export
-linx_rmd <- function(sample, table_dir, plot_dir, out_file = NULL, quiet = FALSE) {
-  assertthat::assert_that(
-    is.character(sample), nchar(sample) > 0,
-    dir.exists(table_dir), dir.exists(plot_dir),
-    quiet %in% c(FALSE, TRUE)
-  )
-  if (!is.null(out_file)) {
-    assertthat::assert_that(
-      is.character(out_file),
-      tools::file_ext(out_file) == "html"
-    )
-  } else {
-    out_file <- glue::glue("linx_{sample}.html")
-  }
-  tmp_dir <- tempdir()
-  rmd_dir <- system.file("rmd/linx", package = "gpgr")
-  cpdir(table_dir, tmp_dir)
-  cpdir(plot_dir, tmp_dir)
-  cpdir(rmd_dir, tmp_dir)
-  rmd_file <- file.path(tmp_dir, "linx", "linx.Rmd")
-  out_dir <- dirname(out_file)
-  mkdir(out_dir)
-  pars <- list(
-    table_dir = table_dir,
-    plot_dir = plot_dir,
-    sample = sample
-  )
-  # suppress DT large size warning
-  options(DT.warn.size = FALSE)
-  rmarkdown::render(
-    input = rmd_file,
-    params = pars,
-    output_dir = out_dir,
-    output_file = I(out_file),
-    run_pandoc = TRUE,
-    quiet = quiet
-  )
-}
-
 #' Generate UMCCR Cancer Report
 #'
 #' Generates a UMCCR Cancer Report. It does so with the following steps:

README.Rmd

@@ -40,15 +40,6 @@ conda install r-gpgr -c umccr -c conda-forge -c bioconda
 
 ## Main modules
 
-### 🕸 LINX {#id_-linx}
-
-- Generate a HTML report with results from the `LINX` structural variant
-  visualisation tool from the Hartwig Medical Foundation
-  (<https://github.com/hartwigmedical/hmftools/tree/master/linx>).
-  See the [CLI](#cli) section below for options.
-- For useful functions for reading/processing `LINX` results, see the vignette at
-  <https://umccr.github.io/gpgr/articles/linx.html>.
-
 ### 🔮 PURPLE {#id_-purple}
 
 - Read and process output files from the `PURPLE` purity/copy number estimator
@@ -89,10 +80,6 @@ echo "#-----------------------------------#"
 echo "gpgr.R --help" & gpgr.R --help
 echo ""
 echo "#-----------------------------------#"
-echo "#------- LINX Report -------#"
-echo "gpgr.R linx --help" & gpgr.R linx --help
-echo ""
-echo "#-----------------------------------#"
 echo "#------- Cancer Report -------#"
 echo "gpgr.R canrep --help" & gpgr.R canrep --help
 echo ""

inst/cli/gpgr.R

@@ -12,19 +12,15 @@ p$add_argument("-v", "--version", action = "version", version = glue::glue("{pro
 subparser_name <- "subparser_name"
 subp <- p$add_subparsers(help = "sub-command help", dest = subparser_name)
 
-source(system.file("cli/linx.R", package = "gpgr"))
 source(system.file("cli/canrep.R", package = "gpgr"))
 
-linx_add_args(subp)
 canrep_add_args(subp)
 
 args <- p$parse_args()
 if (length(args$subparser_name) == 0) {
   p$print_help()
-} else if (args$subparser_name == "linx") {
-  linx_parse_args(args)
 } else if (args$subparser_name == "canrep") {
   canrep_parse_args(args)
 } else {
-  stop("Need to specify 'linx' or 'canrep' in the cli...")
+  stop("Need to specify 'canrep' in the cli...")
 }