WangLabCSU · Yunuuuu · Sep 19, 2025 · Jun 4, 2025 · Jun 4, 2025 · Jun 10, 2025
diff --git a/NAMESPACE b/NAMESPACE
@@ -10,6 +10,7 @@ export(arg0)
 export(bcftools)
 export(bedtools)
 export(bowtie2)
+export(bwa)
 export(cellranger)
 export(cmd_background)
 export(cmd_conda)

diff --git a/R/cmd-bwa.R b/R/cmd-bwa.R
@@ -0,0 +1,48 @@
+#' Run BWA
+#'
+#' BWA is a software package that aligns low-divergence sequences to a
+#' large reference genome, such as the human genome
+#' @param subcmd Sub-Command of BWA (e.g., "index", "mem").
+#' @param ... `r rd_dots("bwa")`.
+#' @param bwa `r rd_cmd("bwa")`.
+#' @inherit exec return
+#' @seealso
+#' - <http://bio-bwa.sourceforge.net/>
+#'
+#' `r rd_seealso()`
+#' @examples
+#' \dontrun{
+#' # Index reference genome
+#' bwa("index", "-a", "bwtsw", "reference.fa") |>
+#'   cmd_run()
+#'
+#' # Paired-end sequence alignment
+#' bwa("mem", "-t", "4", "reference.fa", "read1.fq", "read2.fq") |>
+#'   cmd_run(stdout = "output.sam")
+#'
+#' # Single-end alignment (generate sai file)
+#' bwa("aln", "-t", "4", "reference.fa", "read.fq") |>
+#'   cmd_run(stdout = "read.sai")
+#' }
+#' @family command
+#' @export
+bwa <- make_command(
+  "bwa",
+  function(subcmd = NULL, ..., bwa = NULL) {
+    assert_string(subcmd, allow_empty = FALSE, allow_null = TRUE)
+    assert_string(bwa, allow_empty = FALSE, allow_null = TRUE)
+    BWA$new(cmd = bwa, ..., subcmd = subcmd)
+  }
+)
+
+BWA <- R6Class(
+  "BWA",
+  inherit = Command,
+  private = list(
+    alias = function() "bwa",
+    setup_help_params = function() "--help",
+    combine_params = function(subcmd) {
+      c(subcmd, super$combine_params())
+    }
+  )
+)
diff --git a/blit.Rproj b/blit.Rproj
@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 LineEndingConversion: Posix

diff --git a/man/allele_counter.Rd b/man/allele_counter.Rd
diff --git a/man/bcftools.Rd b/man/bcftools.Rd
diff --git a/man/bedtools.Rd b/man/bedtools.Rd
diff --git a/man/bowtie2.Rd b/man/bowtie2.Rd
diff --git a/man/bwa.Rd b/man/bwa.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/snpEff.Rd b/man/snpEff.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
@@ -8,6 +8,13 @@ testthat::test_that("`bedtools()` works as expected", {
     bedtools() |> cmd_help()
 })
 
+testthat::test_that("`bwa()` works as expected", {
+  testthat::skip_if_not(nzchar(Sys.which("bwa")))
+  bwa() |> cmd_help()
+  bwa("index") |> cmd_help()
+  bwa("mem") |> cmd_help()
+})
+
 testthat::test_that("`cellranger()` works as expected", {
     testthat::skip_if_not(nzchar(Sys.which("cellranger")))
     cellranger() |> cmd_help()
@@ -96,4 +103,30 @@ testthat::test_that("`bcftools()` works as expected", {
 testthat::test_that("`bowtie2()` works as expected", {
   testthat::skip_if_not(nzchar(Sys.which("bowtie2")))
   bowtie2() |> cmd_help()
-})
+})
+
+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()
+})