The intermediate output file still exists

usegalaxy.eu support
2

Hi @chenqiang

As a guess, the files are used in later steps since those are the post-QA core fastqsanger data, correct?

Read files are usually the largest files in any analysis and can definitely explode the quota usage.

Try this if quota space is limited:

  1. Remove the raw read files after QA steps
  2. Keep processed read files for downstream steps like mapping or assembly
  3. After those steps are completed, you can then remove any non-result files.
  4. Dataset files organized into collections with different shapes do not consume extra quota space, since those are just references to the original files.
  5. But if you introduce any changes to metadata or the file contents, those will then become new independent files that do consume quota.

In short, if you want a tool to work on a datasets, it needs to be retained until that tool completes. Once a file is not needed for any downstream tools, you can safely remove it.

You’ll have a copy of the raw files at the original pre-Upload-to-Galaxy source, so those are not needed on the server, correct?

Xref prior related Q&A – the Running Galaxy workflows — Planemo 0.75.20 documentation help is what to review next. Or, maybe review some Published Galaxy workflows? Find the search on the Workflow link in the masthead of the web application.