Question: CWL :Append the ref input used in toolkit
0
gravatar for lizhichao
7 days ago by
lizhichao10
lizhichao10 wrote:

I want the input ref used in analysis toolkit, and the toolkit input the ref in config format,not in command-line format.Then,How can I deal with it,when I use CWL . Thank you!

cwl • 112 views
ADD COMMENTlink modified 3 days ago by Michael R. Crusoe1.5k • written 7 days ago by lizhichao10
1

Hi lizhichao

Your question is too vague and badly written. For people here to help you, you need to explain what you are asking in a well structured way

Please read these post and re-frame the question

How To Ask Good Questions On Technical And Scientific Forums

Brief Reminder On How To Ask A Good Question

ADD REPLYlink modified 7 days ago • written 7 days ago by Vijay Lakhujani4.1k

And I want to know. when cwl running in a docker ,where is the running dir and the input files dir copied to the same dir?

ADD REPLYlink written 7 days ago by lizhichao10

My software need the ref directory name,and I need assign the directory name by cwl-yaml's ref params.How can I achieve it?

ADD REPLYlink written 7 days ago by lizhichao10

It is really difficult to understand what the issue is. Maybe try giving us a specific example of what you are working on. What software do you want to run? Can you post the current version of your command line tool, even if it doesn't work? What is the file you have trouble passing to the tool?

If you put a little more effort into elaborating, i am sure we will be able to help.

ADD REPLYlink written 7 days ago by Tom250

Sorry for my obscure expression. I have made it.

ADD REPLYlink written 22 hours ago by lizhichao10
2
gravatar for Michael R. Crusoe
3 days ago by
Common Workflow Language project
Michael R. Crusoe1.5k wrote:

Hello lizhichao,

For creating configuration files at runtime, please consult this part of the CWL User Guide: https://www.commonwl.org/user_guide/14-runtime/index.html

ADD COMMENTlink written 3 days ago by Michael R. Crusoe1.5k
1

Yes,I have made it. Another quesiton: How can I write inputs to support the one options or more repeats arguments. For example :"-L chr1" and "-L chr1 -L chr2 -L chr3".

ADD REPLYlink written 22 hours ago by lizhichao10

try:

type: string[]
inputBinding:
  prefix: -L
ADD REPLYlink written 20 hours ago by Michael R. Crusoe1.5k

hoping your reply,not vote... Thanks!

ADD REPLYlink written 21 hours ago by lizhichao10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 934 users visited in the last hour