Creating input file(s)

Let us use the same example described in the overview section. We start by getting a set of commands we would like to run.

## wait for a few seconds…
sleep 5
sleep 5

## create two small files
cat $RANDOM > tmp1
cat $RANDOM > tmp2

## merge the two files
cat tmp1 tmp2 > tmp

## check the size of the resulting file
du -sh tmp

Wrap these commands into R

sleep=c('sleep 5', 'sleep 5')

tmp=c('cat $RANDOM > tmp1', 
            'cat $RANDOM > tmp2')
            
merge='cat tmp1 tmp2 > tmp'
            
size='du -sh tmp'

Next, we would create a table using the above commands:

## create a table of all commands
library(flowr)
lst = list( sleep=sleep, 
           create_tmp=tmp, 
           merge=merge,
           size=size)

flowmat = to_flowmat(lst, "samp1")
kable(flowmat)
samplename jobname cmd
samp1 sleep sleep 5
samp1 sleep sleep 5
samp1 create_tmp cat $RANDOM > tmp1
samp1 create_tmp cat $RANDOM > tmp2
samp1 merge cat tmp1 tmp2 > tmp
samp1 size du -sh tmp

Creating Flow Definition

We have a few steps in a pipeline; we would use a flow definition to describe their flow. Flowr enables us to quickly create a skeleton flow definition using a flowmat, which we can then alter to suit our needs. A handy function to_flowdef, accepts a flowmat and creates a flow definition.

## create a skeleton flow definition
def = to_flowdef(flowmat) 
suppressMessages(plot_flow(def))

We can make a few changes to make this pipeline a little more efficient. Briefly, we would run a few steps in a scatter fashion (in parallel).

A few points to note:

  • Initial steps have no dependency, so their previous_jobs and dependency_type is none.
  • Steps with multiple commands, which can be run in parallel are submitted as scatter.
  • Steps with single commands are submitted as serial.
  • Say two consecutive steps run on small pieces of data, we have a serial one to one relationship. Example, both sleep and create_tmp are submitted as scatter and create_tmp has a dependency_type serial.
  • Finally if a step needs all the small pieces from a previous step, we use a gather type dependency.
##               sleep     create tmp   merge     size
def$sub_type = c("scatter", "scatter", "serial", "serial")
def$dep_type = c("none", "serial", "gather", "serial")
kable(def)
jobname sub_type prev_jobs dep_type queue memory_reserved walltime cpu_reserved nodes platform jobid
sleep scatter none none short 2000 1:00 1 1 torque 1
create_tmp scatter sleep serial short 2000 1:00 1 1 torque 2
merge serial create_tmp gather short 2000 1:00 1 1 torque 3
size serial merge serial short 2000 1:00 1 1 torque 4

Create flow, submit to cluster

Next, we create a flow object:

fobj = to_flow(flowmat, def, flowname = "sleep_pipe")

Finally, we can submit this to the cluster:

plot_flow(fobj)
submit_flow(fobj) ## dry run
fobj2 = submit_flow(fobj, execute = TRUE) ## submission to LSF cluster

## after submission, we can use the following:
status(fobj2) ## check status
rerun(fobj2)  ## re-run from a intermediate step
kill(fobj2)   ## kill it!

Creating modules

We used a simple example where a single function was creating all the commands. This is easier, but a step (or module) is not re-usable in another pipeline. Thus we may write a module for each step, such that one may mix and match to create their own pipeline.

NOTE: A module, always returns a flowmat. A module may have one or several steps. A module + flowdef, becomes a pipeline.

## to follow this tutorial, you may download them:
url=https://raw.githubusercontent.com/sahilseth/flowr/master/inst/pipelines
cd ~/flowr/pipelines
wget $url/sleep_pipe.R ## A R script, with sleep_pipe(), which creates a flowmat
wget $url/sleep_pipe.def ## A tab-delimited flow definition file
wget $url/sleep_pipe.conf ## An *optional* tab-delim conf file, defining default params

The sleep_pipe calls the three other functions (modules); fetches flowmat from each, then rbinds them, creating a larger flowmat. You may refer to the sleep_pipe.R file for the source.

Execute the pipeline

Using run

One may use run function to create the flowmat, fetch the flowdef and execute the pipeline in a single step. Here we would focus more on each of these steps in detail.

## 1. Single step submission:
fobj = run("sleep_pipe", execute = TRUE); 

## 2
## change wd, so that we can source the files downloaded in the previous step
setwd("~/flowr/pipelines")

## 2a. optionally, load default parameters
load_opts("sleep_pipe.conf") 

## 2b. get sleep_pipe() function
source("sleep_pipe.R") 
## create a flowmat
flowmat = sleep_pipe()

## 2c. read a flow definition.
flowdef = as.flowdef("sleep_pipe.def")

## 2d. create flow and submit to cluster
fobj = to_flow(flowmat, flowdef, execute = TRUE)

Best practices for writing modules/pipelines

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

picard_merge <- function(x, 
                        samplename = opts_flow$get("samplename"),
                         mergedbam,
                         java_exe = opts_flow$get("java_exe"),
                         java_mem = opts_flow$get("java_mem"),
                         java_tmp = opts_flow$get("java_tmp"),
                         picard_jar = opts_flow$get("picard_jar")){
    ## Make sure all args have a value (not null)
    ## If a variable was not defined in a conf. file opts_flow$get, 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))
}
  1. should accept minimum of two inputs,
    • x (a input file etc, depends on the module) and
    • samplename (is used to append a column to the flowmat)
  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
  3. can define all other default arguments such as paths to tools etc. in a separate conf (tab-delimited) file.
  • Then use opts_flow$get("param") to use their value.
## Example conf file:
cat my.conf
bwa_exe /apps/bwa/bin/bwa
  1. should use check_args() to make sure none of the default parameters are null.
## check_args(), checks ALL the arguments of the function, and throws a error. use ?check_args for more details.
opts_flow$get("my_new_tool")
## NULL

Pipeline structure

For example we have a pipeline consisting of alignment using bwa (aln1, aln2, sampe), fix rg tags using picard and merging the files. We would create three files:

fastq_bam_bwa.R      ## A R script, with fastq_bam_bwa(), which creates a flowmat
fastq_bam_bwa.conf   ## An *optional* tab-delim conf file, defining default params
fastq_bam_bwa.def    ## A tab-delimited flow definition file

Notice how all files have the same basename; this is essential for the run function to find all these files.

  1. all three files should have the same basename

Reason for using the same basename:

  • When we call run("fastq_bam_bwa", ....) it tries to look for a .R file inside flowr’s package, ~/flowr/pipelines OR your current wd. If there are multiple matches, later is chosen.
  • Then, it finds and load default parameters from fastq_bam_bwa.conf (if available).
  • Further, it calls the function fastq_bam_bwa, then stitches a flow using fastq_bam_bwa.def as the flow definition.
  1. can have multiple flowdefs like fastq_bam_bwa_lsf.def, fastq_bam_bwa_lsf.def etc, where .def is used by default. But other are available for users to switch platforms quickly.

Feature:

  • A user can supply a custom flow definition
run('fastq_bam_bwa', def = 'path/myflowdef.def'....)
  • Starting flowr version 0.9.8.9011, run also accepts a custom conf file in addition to a flowdef file. Conf contains all the default parameters like absolute paths to tools, paths to genomes, indexes etc.
run('fastq_bam_bwa', def = 'path/myflowdef.def', conf='path/myconf.conf',....)

This is quite useful for portability, since to use the same pipeline across institution/computing clusters one only needs to change the flow definition and R function remains intact.

Refer to help section on run for more details.

Nomenclature for parameters

Here is a good example: https://github.com/flow-r/flowr/blob/master/inst/pipelines/fastq_bam_bwa.conf

(recommended for increased compatibility)

  1. all binaries end with _exe
  2. all folders end with _dir
  3. all jar files end with _jar
  4. specify cpu’s using <%CPU%>, this makes this value dynamic and is picked up by the flow definition
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