variable inputs workflow

Question: variable inputs workflow

3.7 years ago by

Hello,

I'm trying to create a workflow that has a tool with variable number of inputs. I've searched on this forum to some help but all the questions about that were made about 3 years ago. I'm wondering if you already solved this problem.

Thanks in advance,

Mateus

workflow variable inputs • 1.4k views

ADD COMMENT • link •

modified 3.7 years ago by Guy Reeves • 1.0k • written 3.7 years ago by mateusbellomo • 10

Is the input always the same?

ADD REPLY • link written 3.7 years ago by Bjoern Gruening ♦ 5.1k

If you mean the same format then yes. The content is different. The user could select variable number of files to input in the tool.

ADD REPLY • link written 3.7 years ago by mateusbellomo • 10

Hi Mateus

It might be worth you looking at this recent comment, I think it might also be a solution to this.

C: Creating a Workflow for Variant Detection for 200 samples

But i might have misunderstood.Thanks Guy

ADD REPLY • link written 3.6 years ago by Guy Reeves • 1.0k

3.7 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Hi Mateus

As I understand it there are two data input steps in workflows. The most common is 'Input dataset' and the second is 'Input dataset collection'. Bjoern points to the latter.

But it is also possible to use the 'Input dataset' option by selecting the pile of paper icon upon running the workflow to bring up the option to select a list of files. This recent posting describes a way to input a variable number of files into a work flow (in that case the files are paired).

Linked inputs in created workflow

Thanks Guy

ADD COMMENT • link modified 3.7 years ago • written 3.7 years ago by Guy Reeves • 1.0k

Hi Guy,

I've tried this but when I run the workflow it separates my inputs and run one time for each input in the list. I want to run the workflow for all the inputs in the list in the same flow (only once). To explain better, the first tool of the workflow takes several input files and generate one output that will be used in next steps.

Thanks

ADD REPLY • link written 3.6 years ago by mateusbellomo • 10

Is there always the same number of starting datasets that are ultimately combined into the final outputs? Why not have multiple 'Input dataset' steps at the beginning of you workflow. For example I have 4 to handle the 4 lanes on my NextGen sequencing machine. Will that work.?

ADD REPLY • link written 3.6 years ago by Guy Reeves • 1.0k

I just figured it out how to do it. \o

I used the data set collection and created a list of the input files. This way I the user could select variable number of inputs, create a list and run the workflow after.

Thank you all for the help!

ADD REPLY • link written 3.6 years ago by mateusbellomo • 10

3.7 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

have you tried to use data-collections?

https://wiki.galaxyproject.org/DevNewsBriefs/2014_06_02?highlight=%28collections%29#Dataset_Collections

Cheers,

Bjoern

ADD COMMENT • link written 3.7 years ago by Bjoern Gruening ♦ 5.1k

The problem is that this input is inside a repeat tag where the user have to specify some another information about that input. I think I couldn't solve this problem using data-collections since that's not just a file that the user has to input.

Thanks

ADD REPLY • link written 3.6 years ago by mateusbellomo • 10

Please log in to add an answer.

Similar posts • Search »