Blog post: Moving workflows from single files to collections - a case study

content/news/2023-06-from-single-files-to-collections/index.md

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+---
+title: "Moving workflows from single files to collections - a case study"
+date: "2023-06-20"
+tease: "Allowing a complex workflow to be used on multiple datasets using collections."
+hide_tease: false
+authors: 'Paul Zierep, Engy Nasr'
+authors_structured:
+- github: paulzierep
+- github: EngyNasr
+tags: [EU]
+subsites: [all-eu]
+main_subsite: eu
+---
+
+Collections are a great way to bundle multiple dataset into single entities (as shown in the histroy) that can be 
+processed collectively. In fact, when the amount of datasets rises up to 1000+ it becomes essential to use collections.
+Galaxy can also use collections in tools that are not specifically designed to process 
+collections using the mapping-over strategy (run the tool for each of the elements in a collection). 
+Therefore, it should be a peace of cake to port complete workflows that 
+were based on processing single files to use collections as well.
+However, when applying this idea on our latest metagenomics workflow  [Foodborn Pathogen detection](https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/pathogen-detection-from-nanopore-foodborne-data/tutorial.html) we encountered some problems 
+that arise when switching from single files to collection. 
+In the following we would like to present some of those issues and how we solved them, in the hopes that these strategies can help
+others to port their workflows to collections.
+
+