Concatenation of RNA_Seq technical replicates

[jennaj]

Hi @rcaudle

There were some complications during the recent release cycle (25.0 Galaxy Release (June 2025) — Galaxy Project 25.0.2.dev0 documentation) but we expect that processing should be back to stable now.

Would you be able to try again then let us know if that works as expected or not? You can share back the history if there is some problem and I’ll review. A history with just a small representative sample would be ideal but however you want to report this will be fine.

I may also have alternative processing suggestions. There is a new way to compare collections that doesn’t involve uncompressing/recompressing the individual files repeatedly that may be a more robust solution.

Details were in this topic yesterday:

@jennaj

The tools that seem to be better choices are these:

• Nested Cross Product << NEWER
• Merge collections
• Collapse Collection into single dataset in order of the collection

And, the new collection type:

• Nested Collection (lists of lists) << NEWER

This would work on the collection files directly using the element identifiers, without needing to open the files to read the sequence identifiers, and should be faster and maybe more reliable, especially if these are single-cell data with the really long > title lines. Uncompressing the data would be avoided entirely until the final collapse step.

The other option is try with uncompressed data throughout the early sorting steps when the files are being read repeatedly, then compressing the result at the very end.

Please give this a try and we can follow up to get you to a solution!