I am trying to combine paired-end data into a collection for use in the tool: Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) (Galaxy Version 1.46.0). I uploaded the files individually and tried creating a collection a few ways.
First, I selected all files (24) and created a “list of pairs.” This seemed to work well (it created a list of 12 pairs), but I cannot get the Stacks: de novo map tool to recognize this list as a valid type of input.
Next, I tried to build a collection using rules, but could not figure out how to pair the files, so it ended up creating a list of 24 files. The tool recognized this collection, but I didn’t want to proceed without pairing the data.
Finally, I tried selecting each pair of files, building a dataset pair for each, and then combining these into a collection…but apparently you cannot build a collection from lists of data?
So, my questions are:
Is there a Collection operation I need to use in order to proceed using the “list of pairs?” One that will make the tool recognize the list as a valid collection to input?
OR
Is there a way to pair files when building a collection from rules?
The currently wrapped version of Stacks (version implied is 1.0) does not accept pair-end reads, or rather, not directly as a paired dataset (individual dataset or collection datasets). Inputs are expected to represent R1 reads, either as individual datasets or in a list collection. This means that a paired-end collection won’t be recognized by the tool as a proper input. Please see the manual link below for details – including how to perform the analysis on certain types of paired-end data.
There is an updated version of the underlying tool: Stacks 2.0. It does accept pair-end data directly. However, Stacks 2.0 has not been wrapped for Galaxy (yet) but there is development in progress for this update. I would expect that pair-end collections would be accepted as an input in this version once completed. Please see this IUC issue ticket and related linked discussions/code changes (PRs) for status: https://github.com/galaxyproject/tools-iuc/issues/2073
The accepted inputs for the two two tool versions are explained in the manuals here under the section “What types of data does Stacks (or Stacks 2.0) support?”:
Thanks so much for your response. I hadn’t realized the currently wrapped version was 1.0–that makes sense why it wasn’t accepting my paired-end data! I will try going ahead with just the forward reads.