Attempting to use MultiQC to visualize alignment with HISAT2 but the HISAT2 output collection does not appear

[jennaj]

Hello @rmwade1786 @ypo @StefaniaMontesinos

Please see this prior Q&A:

@jennaj

To output statistics directly from HISAT2 , that output option needs to be set to “Yes” on the tool form. Find it nested under the section “Summary Options”. This would allow you to use MultiQC to compare multiple BAM results together in a single report.

Galaxy has had some interface style updates since the original post, but the optional output toggle is still in the same place on the tool form, and will look like this:

Hope that helps everyone!