Feeding Collections to HISAT2 workflow

Hey all,

I think there is a problem in Galaxy. I am trying to feed some data into my workflow but it doesn’t work. Let me explain. So I have a collection of paired-end data (fastq-dump). The following options in HISAT2 are: Single-end, Paired-end, Paired-end Dataset Collection, Paired-end data from single interleaved dataset.

I chose Paired-end Dataset Collection in HISAT2 to build my workflow

But I can’t connect them. It says: Incompatible collection type(s) for attachment.

However, outside the workflow, I don’t have a problem uploading the fastq-dump in HISAT2 with the Paired-end Dataset Collection setting. Why this discrepancy?Is it because of the fastq-dump?

Also, is there any difference like this: (instead of choosing Paired-end Dataset Collection)

Anyway, one more point: feeding collection into HISAT2 workflow is almost impossible.
Situation 1:

My paired-end collection is not seen

Situation 2:

Same. It won’t let me select my data.

The only way that I found so far to have an workflow with HISAT2 was to choose Paired-end data from single interleaved dataset. But this means that I have to use Fastq-Interlacer on my raw samples before aligning them which takes so much time. I decided to give up on that.

I should add that my workflow is not really complex. I have the input --> HISAT2 --> Filter SAM/BAM tool --> Merging BAMs. (The last step is not essential. It may or may not be there for now at least).

Sorry for the long post. I hope is understandable and is making sense.

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Then that is probably true. Make sure you set the input collection to either “paired” or “list:paired”, not “list” on the right hand side

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You mean here?

Yes, of course I’ve done this. What I said above was: In spite of doing this, it’s not working.

You’re looking at the tool module, I’m talking about the input module.

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Cool. Thanks. Totally missed that