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.
My paired-end collection is not seen
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.