Update HISAT2 DM for normalized layout, plus other fixes:

[natefoo]

• Drop python wrapper
• Update HISAT2 version
• Add test of (some) non-default options

I apparently missed this one in #6489.

Other stuff:

• Fix data table entry for Bowtie2 DM
• Do not include sequence (link, or in DM bundles, copy) in output of BWA-MEM1/2, Bowtie1/2, and HISAT2 DMs

FOR CONTRIBUTOR:

• [x] I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• [x] License permits unrestricted use (educational + commercial)
• [ ] This PR adds a new tool or tool collection
• [x] This PR updates an existing tool or tool collection
• [ ] This PR does something else (explain below)

[natefoo]

The 403s seem to be deliberate blocks of GHA, as such I am not sure how to proceed.

[bernt-matthias]

The 403s seem to be deliberate blocks of GHA, as such I am not sure how to proceed.

Definitely ignore - its not your fault. Apparently many sites do this. Sometimes I replaced citation links with links to pubmed - but it feels wrong. Contacting them 1 by one?

In the worst case we push manually to the TS.

[bernt-matthias]

Two tests seem to fail.

[bernt-matthias]

The 403s seem to be deliberate blocks of GHA, as such I am not sure how to proceed.

... Sometimes I replaced citation links with links to pubmed - but it feels wrong.

Hopefully this is a cleaner solution.

[bgruening]

Is it ok, if I merge this?

[bernt-matthias]

Yes, but needs to be pushed manually.

[mvdbeek]

Attention: deployment skipped!

https://github.com/galaxyproject/tools-iuc/actions/runs/17009192367

[bgruening]

Uploaded.

[natefoo]

Thank you @bernt-matthias and @bgruening!