Question: How to run a workflow using Dataset Collection?
0
gravatar for northcoted
2.1 years ago by
northcoted30
northcoted30 wrote:

HI,

I created a workflow which has as input a dataset collection which consists of 12 BAM Files.

However when I extract the workflow for editing, save and then run it, the "Input Dataset Collection" field simply says "No data dataset collection available.".

This is produced when only selecting the dataset collection as input and ignoring the dataset collections input datasets in the "Create Workflow" interface.

However, if I select the dataset collection and all of the input datasets, the interface requests that I choose each input file for each step.

Am I going about this the wrong way?

software error • 756 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by northcoted30
1
gravatar for northcoted
2.1 years ago by
northcoted30
northcoted30 wrote:

Hi.

The following images shows the "lack of" progression of my workflow build and might better explain my problem.

The 1st image shows the workflow editor, which was built via the "extract workflow" function of the "analyze data" option.

Extracted WORKFLOW

The second image is an attempt to run this workflow, however please note that it claims that there are no dataset collection.

RUN Workflow

This is the problem.

I would be grateful for any input.

Regards

Derek

ADD COMMENTlink written 2.1 years ago by northcoted30

Hi Derek,

Are you able to reproduce this at http://usegalaxy.org? If so, please share the workflow and history by generating a link and sending these in an email to galaxy-bugs@lists.galaxyproject.org. Please include a link to this Biostars post in the message.

If this can be reproduced with a smaller history/workflow, that is best when sharing this way and will be easier to review.

The other route is to make certain that you are running the latest Galaxy build (v 16.04). There are many improvements in the code base and staying current is the best way for us to diagnose the root cause of a problem. If running another build/version, you can share that, too.

Thanks, Jen, Galaxy team

ADD REPLYlink written 2.1 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

For the initial problem, perhaps the starting history does not contain a dataset collection with the appropriate "datatype" specified?

The rest sounds like an editor problem. Examine the workflow within the editor and double check that the jobs are linked (by "noodles" that are rendered like banded ribbons for dataset collections).

I'll also run a test here and our team will write back if there is more going on.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k

Thanks. I'll give it a try and get back to you.

Cheers

Derek

ADD REPLYlink written 2.1 years ago by northcoted30
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