macs2-callpeak Command Line Tool definition

[alexbarrera]

MACS2 callpeak subcommand CWL definition. Compared with the original MACS2 callpeak command, the only difference is the usage of the first treatment sample as basename for the output files produced (-n parameter).

[mr-c]

Thank you @alexbarrera for your contribution. I left a question in-line about the availability of long-form options.

[alexbarrera]

Hi @mr-c. There are --treatment and --control instead of -t and -c. Are long forms preferred over short ones?

[mr-c]

From a readability and debugging perspective I recommend them. We don't (yet) have a formal style guide.

On Mon, May 9, 2016 at 6:12 PM, Alejandro Barrera notifications@github.com wrote:

Hi @mr-c https://github.com/mr-c. There are --treatment and --control instead of -t and -c. Are long forms preferred over short ones?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/common-workflow-language/workflows/pull/81#issuecomment-217911035

Michael R. Crusoe michael.crusoe@gmail.com Community Engineer Common Workflow Language project https://impactstory.org/u/0000-0002-2961-9670 +32 (0) 2 808 25 58 +1 480 627 9108

[portah]

I like this CWL description, we are going to use it :) soon. @mr-c the only question that I have is about docker, I'm okey with ubuntu's package. However, we already use the latest github version. How we can deal with this in the future?

[mr-c]

@portah has the CLI interface changed between the two versions? You can always backport a newer package to any Debian or Ubuntu supported release

[mr-c]

Thank you @alexbarrera !

[alexbarrera]

@mr-c no problem!