common-workflow-language

CWL documents describe workflows made of command line data analysis tools in a portable, reproducible, and reusable fashion.

As requested in https://gitter.im/bd2k-genomics-toil/Lobby?at=617126297db1e3753e527ff2 it would be useful for debugging to be able to stop the whole workflow as soon as a single job fails, even if other jobs still exist to be run or are currently running.

┆Issue is synchronized with this Jira Task
┆Issue Number: TOIL-1062

Expected Behavior

cwltool ignores default values when using the argument on the command line

Actual Behavior

Calling cwltool with an argument that is a string[] in the command line will keep the the default value in the array.
Does not happen when using a yaml file as input.

Workflow Code

#!/usr/bin/env cwl-runner

cwlVersion: v1.2
class: CommandLineTool

baseCommand:

Can someone explain to me how to use InitialWorkDir requirements without any input parameters.
For instance, I need to put my shell scripts near with cwl script and run them from that cwl script. Is there some way don't use absolute path to scripts? I tried to use EnvVariable like that:

baseCommand: sh
arguments: [$SCRIPT_FOLDER/script.sh]

But it is not working.

Then I foun

Either via Python libraries, or handing off to 3rd party tools

DOI to bibtex
conda & Debian package name to bibtex
bio.tools identifier to bibtex
RRID to bibtext

Description

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References

http://docs.ogc.org/DRAFTS/18-062.html#_link_headers

common-workflow-language

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