Question: How to run a workflow using Dataset Collection?
gravatar for northcoted
23 months ago by
northcoted30 wrote:


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 • 651 views
ADD COMMENTlink modified 22 months ago • written 23 months ago by northcoted30
gravatar for northcoted
22 months ago by
northcoted30 wrote:


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.



ADD COMMENTlink written 22 months ago by northcoted30

Hi Derek,

Are you able to reproduce this at If so, please share the workflow and history by generating a link and sending these in an email to 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 22 months ago by Jennifer Hillman Jackson24k
gravatar for Jennifer Hillman Jackson
23 months ago by
United States
Jennifer Hillman Jackson24k wrote:


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 23 months ago by Jennifer Hillman Jackson24k

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



ADD REPLYlink written 23 months ago by northcoted30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 152 users visited in the last hour