Question: Workflow with collections
gravatar for agatyr
21 days ago by
agatyr20 wrote:

The task was to download several SRAs from NCBI, align to reference genome, find SNPs. I made many attempts to use collections in workflow, but it broke at some point. When I tried to figure out the cause of it I come to following observation: when I use BWA-MEM manually, point it to "list of pairs" collection and reference genome FAS, it works. But if I make a simple test workflow with only BWA-MEM step, and use the same files upon run, it does not appear in History, and nothing happened. Is it bug, or am I doing something wrong?

ADD COMMENTlink modified 19 days ago • written 21 days ago by agatyr20
gravatar for Jennifer Hillman Jackson
19 days ago by
United States
Jennifer Hillman Jackson24k wrote:


Several of your mini-workflows do not include an Inputs dataset. I do see Inputs included in the larger workflows.

Try adding one in, connect it to the downstream tool or tools, and rerun. Choices for Inputs types are at the very top of the tool panel within the workflow editor.


  • Input dataset
  • Input dataset collection

This may be a bug - I am checking with the development team. Not including Inputs will work for individual datasets when selected at runtime, but not collections datasets. If we make an issue ticket, I'll link it back as a comment.

There is another issue with workflows related to tool version conflicts we are working on. The workaround (until fixed) is to connect all noodles for tools in the editor left-to-right (input noodles, then output noodles, per tool). This may have been part of your problem with the larger workflow. Try reconnecting the noodles in this way and the version problem will not be a factor when you are tuning/troubleshooting the larger workflow.

Thank for reporting the problem! Jen, Galaxy team

ADD COMMENTlink modified 19 days ago • written 19 days ago by Jennifer Hillman Jackson24k
gravatar for agatyr
19 days ago by
agatyr20 wrote:

Thank you Jen!

I've figured out the problem with left-to-right connections, and I override it using copying of the downstream blocks and reconnecting, it's OK. But I tried to use input for BWA-MEM, and I cannot connect the "Input dataset collection" to "Select a paired collection", it does not turn green. If I select other types of the input, then I could connect, but it does not work the way I would like, of course. And as I said, manually I do the same BWA-MEM on collections, and it works perfectly.

ADD COMMENTlink modified 19 days ago • written 19 days ago by agatyr20


An Inputs dataset is confirmed as being required when using collections. Our team is deciding how to fix this.

The ticket with all problems detailed is here:

Thank you again for reporting the problems!

ADD REPLYlink modified 19 days ago • written 19 days ago by Jennifer Hillman Jackson24k


The Collection input type needs to be set to be a paired list of datasets. This example workflow has all of the setting correct and the noodles attached:

To reset the "type" click onto the Input box, and in the far right configuration options, click into "Type" and type in some text, the pull-down menu will provide the choices. Only do this once - I had problems when switching the type a few times - we will be also looking into this more.

ADD REPLYlink written 19 days ago by Jennifer Hillman Jackson24k

Many many thanks! Really works now.

ADD REPLYlink written 18 days ago by agatyr20
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