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Contributing

Each file in the R folder represents a tool. In it we have a R function preferably of the same name, or a similar easy name.

These are some of the practices we follow in-house. We feel using these makes stitching custom pipelines using a set of modules quite easy. Consider this a check-list of a few ideas and a work in progress.

A note on module functions

  1. should accept minimum of two inputs,
    • a input file etc, depends on the module. Flexible
    • samplename (is used to append a column to the flowmat)
x
samplename = get_opts("samplename")
  1. should always return a list arguments:
    • flowmat (required) : contains all the commands to run
    • outfiles (recommended): could be used as an input to other tools
return(list(outfiles = mergedbam, flowmat = flowmat))
  1. can define all other default arguments such as paths to tools etc. in a seperate conf (tab-delimited) file.
  • Then use get_opts("param") to use their value.
## Example conf file:
cat my.conf
bwa_exe	/apps/bwa/bin/bwa
  1. should use check_args() to make sure none of the default parameters are null.
## check_args(), checks ALL the arguments of the function, 
## and throws a error. use ?check_args for more details.
get_opts("my_new_tool")

Example

picard_merge <- function(x,
        samplename = get_opts("samplename"),
        mergedbam,
        java_exe = get_opts("java_exe"),
        java_mem = get_opts("java_mem"),
        java_tmp = get_opts("java_tmp"),
        picard_jar = get_opts("picard_jar")){
	
  ## Make sure all args have a value (not null)
  ## If a variable was not defined in a conf. file get_opts, will return NULL
  check_args()  
  
  bam_list = paste("INPUT=", x, sep = "", collapse = " ")
  ## create a named list of commands
  cmds = list(merge = sprintf("%s %s -Djava.io.tmpdir=%s -jar %s MergeSamFiles %s OUTPUT=%s ASSUME_SORTED=TRUE VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true USE_THREADING=true",
  java_exe, java_mem, java_tmp, picard_jar, bam_list, mergedbam))
  
  ## Create a flowmat
  flowmat = to_flowmat(cmds, samplename)
  
  ## return a list, flowmat AND outfiles
  return(list(outfiles = mergedbam, flowmat = flowmat))
}