WangLabCSU · Yunuuuu · Jul 26, 2025 · Jul 4, 2025 · Jul 5, 2025 · Jul 21, 2025
diff --git a/NAMESPACE b/NAMESPACE
@@ -40,6 +40,7 @@ export(trust4)
 export(trust4_gene_names)
 export(trust4_imgt_annot)
 export(uninstall_appmamba)
+export(varscan)
 importFrom(R6,R6Class)
 importFrom(rlang,":=")
 importFrom(rlang,.data)

diff --git a/R/cmd-varscan.R b/R/cmd-varscan.R
@@ -0,0 +1,45 @@
+#' VarScan is a platform-independent software tool 
+#' developed at the Genome Institute at Washington University to detect variants in NGS data.
+#'
+#' @param subcmd Sub-Command of varscan. Details see: `r rd_help("varscan")`.
+#' @param ... `r rd_dots("varscan")`.
+#' @param varscan `r rd_cmd("varscan")`.
+#' @seealso
+#' - <https://varscan.sourceforge.net/>
+#'
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+varscan <- make_command(
+  "varscan",
+  function(
+    subcmd = NULL,
+    ...,
+    varscan = NULL
+    ) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(varscan, allow_empty = FALSE, allow_null = TRUE)
+    Varscan$new(
+      cmd = varscan,
+      ...,
+      subcmd = subcmd
+    )
+  }
+)
+
+Varscan <- R6Class(
+  "Varscan",
+  inherit = Command,
+  private = list(
+    alias = function() "varscan",
+    setup_help_params = function() "help",
+    combine_params = function(subcmd) {
+      if (private$help) {
+        c(super$combine_params(), subcmd)
+      } else {
+        c(subcmd, super$combine_params())
+      }
+    }
+  )
+)
diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
diff --git a/man/cellranger.Rd b/man/cellranger.Rd
diff --git a/man/conda.Rd b/man/conda.Rd
diff --git a/man/exec.Rd b/man/exec.Rd
diff --git a/man/fastp.Rd b/man/fastp.Rd
diff --git a/man/fastq_pair.Rd b/man/fastq_pair.Rd
diff --git a/man/gistic2.Rd b/man/gistic2.Rd
diff --git a/man/kraken2.Rd b/man/kraken2.Rd
diff --git a/man/kraken_tools.Rd b/man/kraken_tools.Rd
diff --git a/man/perl.Rd b/man/perl.Rd
diff --git a/man/pyscenic.Rd b/man/pyscenic.Rd
diff --git a/man/python.Rd b/man/python.Rd
diff --git a/man/samtools.Rd b/man/samtools.Rd
diff --git a/man/seqkit.Rd b/man/seqkit.Rd
diff --git a/man/trust4.Rd b/man/trust4.Rd
diff --git a/man/varscan.Rd b/man/varscan.Rd
diff --git a/tests/testthat/test-exec.R b/tests/testthat/test-exec.R
@@ -66,3 +66,29 @@ testthat::test_that("`pipe()` method works well", {
         cmd_run()
     testthat::expect_identical(read_lines(file), read_lines(file2))
 })
+
+testthat::test_that("`varscan()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("varscan")))
+  varscan() |> cmd_help()
+})
+
+testthat::test_that("`fastp()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("fastp")))
+  fastp() |> cmd_help()
+})
+
+
+testthat::test_that("`snpeff()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("snpeff")))
+  snpeff() |> cmd_help()
+})
+
+testthat::test_that("`bcftools()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bcftools")))
+  bcftools() |> cmd_help()
+})
+
+testthat::test_that("`bowtie2()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bowtie2")))
+  bowtie2() |> cmd_help()
+})