Bowtie2 output data type not recognised in workflow designer

nasos1724 · January 16, 2022, 11:41am

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?

Thanks

bjoern.gruening · January 16, 2022, 1:52pm

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

nasos1724 · January 16, 2022, 1:54pm

On the usegalaxy.eu server.

bjoern.gruening · January 16, 2022, 1:56pm

Can you please share me your workflow?

nasos1724 · January 16, 2022, 2:03pm

Of course.

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

bjoern.gruening · January 16, 2022, 2:34pm

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

mvdbeek · January 16, 2022, 3:19pm

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 ?

nasos1724 · January 16, 2022, 4:22pm

I tried that and I get the same message.

mvdbeek · January 16, 2022, 5:53pm

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.