contributing.md

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

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")

2. 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))

3. can define all other default arguments such as paths to tools etc. in a seperate conf (tab-delimited) file.

4. 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.

{r} ## 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

```{r picard_merge, echo=TRUE, comment=""} 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)) } ```

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.