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Building workflows with the Common Workflow Language.
There are several workflow tools for bioinformatics. Interoperability (the I in FAIR) is however often still a problem. In the context of creating a workflow that can easily migrate an open source workflow from Naturalis (see internship: https://www.rijkzwaancareers.com/careers/joint-internship-bioinformatics-rijk-zwaan-and-naturalis ) we're going to try out the CWL standard by creating a workflow with the Rabix Composer GUI and then running it locally with the CWL reference tool. Since CWL has multiple interpreters (toil, nextflow), it should afterwards be easier to run this workflow anywhere.
Check out the preparation guidelines below
Time and Place
Where: Room D1.113, Science Park 904 When: Tuesday, January 9th, 2018 at 17:00 PM
I think I found the problem. As a temporary solution, you've became a full member so you should have read/write rights. When we're done, I'll try to convert you an outside collaborator with read/write privileges.
Let me know how it goes!
Description
Building workflows with the Common Workflow Language.
There are several workflow tools for bioinformatics. Interoperability (the I in FAIR) is however often still a problem. In the context of creating a workflow that can easily migrate an open source workflow from Naturalis (see internship: https://www.rijkzwaancareers.com/careers/joint-internship-bioinformatics-rijk-zwaan-and-naturalis ) we're going to try out the CWL standard by creating a workflow with the Rabix Composer GUI and then running it locally with the CWL reference tool. Since CWL has multiple interpreters (toil, nextflow), it should afterwards be easier to run this workflow anywhere.
Check out the preparation guidelines below
Time and Place
Where: Room D1.113, Science Park 904
When: Tuesday, January 9th, 2018 at 17:00 PM
Required Preparation
Prior knowledge required
Software Dependencies
Cwltool
( see https://github.com/common-workflow-language/cwltool )
Rabix composer:
https://github.com/rabix/composer/releases/download/v1.0.0-rc.2/rabix-composer-1.0.0-rc.2.zip
(* note: there is also an installer for Mac in case you have a Mac laptop)
A graphical interface will open
Step-by-step activities for the hour
Getting started
Creating a test file, initialize our Rabix workspace and a first tool wrapper
cd rabix-workspace
seq 100 120 > lines.txt
start Rabix composer (see above)
Top left: "My Project" .. "+ Open a Project"
"Local" .. "Select a folder"
Choose "rabix-workspace" .. "Add to workspace"
Double-click on "Local files" at the left pane, the folder should appear.
Press the "+" on the top of the screen to go to the "new file" tab
"New command line tool"
App Name: ReverseLinesStep, CWL 1.0, choose a local folder, your rabix workspace, create
You'll get a new tab
Base command: /usr/bin/rev
Input ports: Add an Input:
required: yes;
ID: input-for-reverselines,
Type: File;
Include in command line: no
Save!
Output ports: Add an Output:
required: yes
ID: output
Glob: output-from-reverselines.*
Save!
Other: stdout redirect: output-from-reverse-lines.txt
Save!
Run the output file in cwltool
Now try eSciencecenter's scriptcwl
Additional reading material
A nice tutorial
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