Bowtie2 output data type not recognised in workflow designer

I was trying to create a workflow that included Bowtie2, however it seems that the output file/s is not recognized as proper input file for MergeSamFiles or featureCounts.
Is this a normal phenomenon?


@nasos1724 on which Galaxy server have you seen this? It seems it missing some datatypes.

On the server.

Can you please share me your workflow?

Of course.

We will investigate. Thanks for reporting. In the meantime please use BWA-mem instead of Bowtie.

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The screenshot shows that you’re trying to connect the bowtie2 output to an input that is already connected, that doesn’t work. Have you tried disconnecting the MergeSamFiles input first ?

I tried that and I get the same message.

Alright, I think we’ve got a fix in [21.09] Fix workflow connections for outputs that are not displayed in uploads by mvdbeek · Pull Request #13174 · galaxyproject/galaxy · GitHub, that should be on the public servers soon.