Robust, flexible and resource-efficient pipelines using Go and the commandline

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Why SciPipe?

• Intuitive: SciPipe works by flowing data through a network of channels and processes
• Flexible: Wrapped command-line programs can be combined with processes in Go
• Convenient: Full control over how your files are named
• Efficient: Workflows are compiled to binary code that run fast
• Parallel: Pipeline paralellism between processes as well as task parallelism for multiple inputs, making efficient use of multiple CPU cores
• Supports streaming: Stream data between programs to avoid wasting disk space
• Easy to debug: Use available Go debugging tools or just println()
• Portable: Distribute workflows as Go code or as self-contained executable files

Project updates

• NEW - The SciPipe paper published open access in GigaScience: SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines
• Scientific study using SciPipe: Predicting off-target binding profiles with confidence using Conformal Prediction
• Slides: Presentation on SciPipe and more at Go Stockholm Conference
• Blog post: Provenance reports in Scientific Workflows - going into details about how SciPipe is addressing provenance
• Blog post: First production workflow run with SciPipe

Introduction

SciPipe is a library for writing Scientific Workflows, sometimes also called "pipelines", in the Go programming language.

When you need to run many commandline programs that depend on each other in complex ways, SciPipe helps by making the process of running these programs flexible, robust and reproducible. SciPipe also lets you restart an interrupted run without over-writing already produced output and produces an audit report of what was run, among many other things.

SciPipe is built on the proven principles of Flow-Based Programming (FBP) to achieve maximum flexibility, productivity and agility when designing workflows. Compared to plain dataflow, FBP provides the benefits that processes are fully self-contained, so that a library of re-usable components can be created, and plugged into new workflows ad-hoc.

Similar to other FBP systems, SciPipe workflows can be likened to a network of assembly lines in a factory, where items (files) are flowing through a network of conveyor belts, stopping at different independently running stations (processes) for processing, as depicted in the picture above.

SciPipe was initially created for problems in bioinformatics and cheminformatics, but works equally well for any problem involving pipelines of commandline applications.

Project status: SciPipe is still alpha software and minor breaking API changes still happens as we try to streamline the process of writing workflows. Please follow the commit history closely for any API updates if you have code already written in SciPipe (Let us know if you need any help in migrating code to the latest API).

Known limitations

• There are still a number of missing good-to-have features for workflow design. See the issue tracker for details.
• There is not (yet) support for the Common Workflow Language.

Hello World example

Let's look at an example workflow to get a feel for what writing workflows in SciPipe looks like:

package main

import (
    // Import SciPipe, aliased to sp
    sp "github.com/scipipe/scipipe"
)

func main() {
    // Init workflow and max concurrent tasks
    wf := sp.NewWorkflow("hello_world", 4)

    // Initialize processes, and file extensions
    hello := wf.NewProc("hello", "echo 'Hello ' > {o:out|.txt}")
    world := wf.NewProc("world", "echo $(cat {i:in}) World > {o:out|.txt}")

    // Define data flow
    world.In("in").From(hello.Out("out"))

    // Run workflow
    wf.Run()
}

Running the example

Let's put the code in a file named scipipe_helloworld.go and run it:

$ go run minimal.go
AUDIT   2018/07/17 21:42:26 | workflow:hello_world             | Starting workflow (Writing log to log/scipipe-20180717-214226-hello_world.log)
AUDIT   2018/07/17 21:42:26 | hello                            | Executing: echo 'Hello ' > hello.out.txt
AUDIT   2018/07/17 21:42:26 | hello                            | Finished: echo 'Hello ' > hello.out.txt
AUDIT   2018/07/17 21:42:26 | world                            | Executing: echo $(cat ../hello.out.txt) World > hello.out.txt.world.out.txt
AUDIT   2018/07/17 21:42:26 | world                            | Finished: echo $(cat ../hello.out.txt) World > hello.out.txt.world.out.txt
AUDIT   2018/07/17 21:42:26 | workflow:hello_world             | Finished workflow (Log written to log/scipipe-20180717-214226-hello_world.log)

Let's check what file SciPipe has generated:

$ ls -1 hello*
hello.out.txt
hello.out.txt.audit.json
hello.out.txt.world.out.txt
hello.out.txt.world.out.txt.audit.json

As you can see, it has created a file hello.out.txt, and hello.out.world.out.txt, and an accompanying .audit.json for each of these files.

Now, let's check the output of the final resulting file:

$ cat hello.out.txt.world.out.txt
Hello World

Now we can rejoice that it contains the text "Hello World", exactly as a proper Hello World example should :)

Now, these were a little long and cumbersome filenames, weren't they? SciPipe gives you very good control over how to name your files, if you don't want to rely on the automatic file naming. For example, we could set the first filename to a static one, and then use the first name as a basis for the file name for the second process, like so:

package main

import (
    // Import the SciPipe package, aliased to 'sp'
    sp "github.com/scipipe/scipipe"
)

func main() {
    // Init workflow with a name, and max concurrent tasks
    wf := sp.NewWorkflow("hello_world", 4)

    // Initialize processes and set output file paths
    hello := wf.NewProc("hello", "echo 'Hello ' > {o:out}")
    hello.SetOut("out", "hello.txt")

    world := wf.NewProc("world", "echo $(cat {i:in}) World >> {o:out}")
    // The modifier 's/.txt//' will replace '.txt' in the input path with ''
    world.SetOut("out", "{i:in|s/.txt//}_world.txt")

    // Connect network
    world.In("in").From(hello.Out("out"))

    // Run workflow
    wf.Run()
}

Now, if we run this, the file names get a little cleaner:

$ ls -1 hello*
hello.txt
hello.txt.audit.json
hello.txt.world.go
hello.txt.world.txt
hello.txt.world.txt.audit.json

The audit logs

Finally, we could have a look at one of those audit file created:

$ cat hello.txt.world.txt.audit.json
{
    "ID": "99i5vxhtd41pmaewc8pr",
    "ProcessName": "world",
    "Command": "echo $(cat hello.txt) World \u003e\u003e hello.txt.world.txt.tmp/hello.txt.world.txt",
    "Params": {},
    "Tags": {},
    "StartTime": "2018-06-15T19:10:37.955602979+02:00",
    "FinishTime": "2018-06-15T19:10:37.959410102+02:00",
    "ExecTimeNS": 3000000,
    "Upstream": {
        "hello.txt": {
            "ID": "w4oeiii9h5j7sckq7aqq",
            "ProcessName": "hello",
            "Command": "echo 'Hello ' \u003e hello.txt.tmp/hello.txt",
            "Params": {},
            "Tags": {},
            "StartTime": "2018-06-15T19:10:37.950032676+02:00",
            "FinishTime": "2018-06-15T19:10:37.95468214+02:00",
            "ExecTimeNS": 4000000,
            "Upstream": {}
        }
    }

Each such audit-file contains a hierarchic JSON-representation of the full workflow path that was executed in order to produce this file. On the first level is the command that directly produced the corresponding file, and then, indexed by their filenames, under "Upstream", there is a similar chunk describing how all of its input files were generated. This process will be repeated in a recursive way for large workflows, so that, for each file generated by the workflow, there is always a full, hierarchic, history of all the commands run - with their associated metadata - to produce that file.

You can find many more examples in the examples folder in the GitHub repo.

For more information about how to write workflows using SciPipe, and much more, see SciPipe website (scipipe.org)!

More material on SciPipe

• See a poster on SciPipe, presented at the e-Science Academy in Lund, on Oct 12-13 2016.
• See slides from a recent presentation of SciPipe for use in a Bioinformatics setting.
• The architecture of SciPipe is based on an flow-based programming like pattern in pure Go presented in this and this blog posts on Gopher Academy.

Citing SciPipe

If you use SciPipe in academic or scholarly work, please cite the following paper as source:

Lampa S, Dahlö M, Alvarsson J, Spjuth O. SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines Gigascience. 8, 5 (2019). DOI: 10.1093/gigascience/giz044

Acknowledgements

• SciPipe is very heavily dependent on the proven principles form Flow-Based Programming (FBP), as invented by John Paul Morrison. From Flow-based programming, SciPipe uses the ideas of separate network (workflow dependency graph) definition, named in- and out-ports, sub-networks/sub-workflows and bounded buffers (already available in Go's channels) to make writing workflows as easy as possible.
• This library is has been much influenced/inspired also by the GoFlow library by Vladimir Sibirov.
• Thanks to Egon Elbre for helpful input on the design of the internals of the pipeline, and processes, which greatly simplified the implementation.
• This work is financed by faculty grants and other financing for the Pharmaceutical Bioinformatics group of Dept. of Pharmaceutical Biosciences at Uppsala University, and by Swedish Research Council through the Swedish National Bioinformatics Infrastructure Sweden.
• Supervisor for the project is Ola Spjuth.

Related tools

Find below a few tools that are more or less similar to SciPipe that are worth worth checking out before deciding on what tool fits you best (in approximate order of similarity to SciPipe):

• NextFlow
• Luigi/SciLuigi
• BPipe
• SnakeMake
• Cuneiform