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bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers
MIT License
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Updating sambamba merge tool: Quick fix for ERGA BGE Galaxy workflow #1433

Closed SaimMomin12 closed 3 months ago

SaimMomin12 commented 3 months ago

Hi @bgruening,

Considering the present state of samtools merge, I think we require more time and efforts to fix and cleanup the wrapper.

In the meantime, until the above is fixed I would propose that we use sambamba merge to circumnavigate the present issues faced in the ERGA BGE Galaxy workflow. With my recent talk with Diego/Tom, they would like to present the ERGA BGE Galaxy workflow in the upcoming GCC. Keep this in mind, I thought of spinning off the sambamba merge to suffice the urgency.

I realized there was already a sambamba tool suite wrapper in your repository developed several years back, but was not put into the EU Galaxy server. I've made some minor changes just in sambamba_merge, updated the tool version and included the relevant test case.

I hope this will help us to tackle the issue just for time being.

TL;DR I've updated the sambamba merge wrapper, included relevant test cases and test the tool. This is quick fix until the samtools merge is fixed. :smiley:

Thanks!

SaimMomin12 commented 3 months ago

It looks like other tools from this suite needs to be updated/fixed too. What do you suggest? I just need the sambamba merge though! :sweat_smile: