Issues Modifying Existing Workflow from SE to PE

1

Hi,

I’d like to modify my workflow from single-end to paired-end, however when I switch the tools to PE compatibility everything breaks. What am I doing wrong?

Workflow: Galaxy
Platform: DNBSEQ-G400RS
Read Layout/Length: PE150, Standard MPS, Whole Genome

Any advice would be greatly appreciated.

Thanks!

1 Like
2

Hi @zpho3nix

Thanks for sharing the workflow, very helpful!

Try this

  1. Before the FastQC step, you’ll need to run Flatten Collection on the paired end input collection as an intermediate step. An example is in this workflow → https://usegalaxy.org/u/jen-galaxyproject/w/quality-control-template

  2. Disconnect all other noodle connections between the other steps, double check that the tool parameters are set for paired end data, then reconnect the noodles in the order of operations, inputs through to downstream. This reconnection resets the metadata between the tools (fixes up the workflow metadata, not the tool options or datatypes!).

    Example: Bowtie2 still has the single end input choice.

    Screen Shot 2025-07-01 at 1.12.15 PM
    Screen Shot 2025-07-01 at 1.12.15 PM1195×652 96.3 KB

Please give that a try and let us know if it helps! You can share back your adjusted workflow for more feedback if anything is still not working. :slight_smile: