Update NEWS.md

NAMESPACE

@@ -7,6 +7,7 @@ export(appmamba)
 export(appmamba_rc)
 export(arg)
 export(arg0)
+export(bowtie2)
 export(bcftools)
 export(cellranger)
 export(cmd_background)

NEWS.md

@@ -2,6 +2,16 @@
 
 * Rename `cmd_conda` to `cmd_codnaenv()`.
 
+* new command `fastp`
+
+* new command `varscan`
+
+* new command `bcftools`
+
+* new command `snpEff`
+
+* new command `bowtie2`
+
 # blit 0.2.0
 
 ## New features

R/cmd-bowtie2.R

@@ -0,0 +1,63 @@
+#' Run bowtie2
+#'
+#' Bowtie 2 is an ultrafast and memory-efficient tool 
+#' for aligning sequencing reads to long reference sequences. 
+#' It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, 
+#' and particularly good at aligning to relatively long (e.g. mammalian) genomes. 
+#' Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: 
+#' for the human genome, its memory footprint is typically around 3.2 GB. 
+#' Bowtie 2 supports gapped, local, and paired-end alignment modes.
+#' 
+#' @param index Path to bowtie2 index prefix (without file extensions).
+#' @param reads A character vector of FASTQ files used as input to bowtie2.
+#' @param ofile A string of path to the output sam file.
+#' @param ... `r rd_dots("bowtie2")`.
+#' @param bowtie2 `r rd_cmd("bowtie2")`.
+#' @family command
+#' @inherit exec return
+#' @seealso
+#' - <https://bowtie-bio.sourceforge.net/bowtie2/index.shtml>
+#'
+#' `r rd_seealso()`
+#' @export
+bowtie2 <- make_command(
+  "bowtie2",
+  function(
+    index,
+    reads,
+    ofile,
+    ...,
+    bowtie2 = NULL
+  ){
+    assert_string(bowtie2, allow_empty = FALSE, allow_null = TRUE)
+    Bowtie2$new(
+      cmd = bowtie2,
+      ...,
+      index = index,
+      reads = reads,
+      ofile = ofile
+    )
+  }
+)
+
+Bowtie2 <- R6Class(
+  "Bowtie2",
+  inherit = Command,
+  private = list(
+    alias = function() "bowtie2",
+    setup_help_params = function() "--help",
+    setup_command_params = function(index, reads, ofile){
+      c(
+        arg0("-x", index),
+        if (length(reads) == 1L){
+          arg0("-U", reads)
+        } else if (length(reads) == 2L){
+          arg0("-1", reads[1], "-2", reads[2])
+        } else {
+          cli::cli_abort("{.arg reads} must be of length 1 or 2")
+        },
+        arg0("-S", ofile)
+      )
+    }
+  )
+)