Bowtie2 output data type not recognised in workflow designer

usegalaxy.eu support
,
1

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?

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Thanks

2

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

3

On the usegalaxy.eu server.

4

Can you please share me your workflow?

5

Of course.

https://usegalaxy.eu/u/rna1724/w/rna-seq-ion-torrent

6

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

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7

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 ?

8

I tried that and I get the same message.

9

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.

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