8000 Adjust for mouse alleles by skrakau · Pull Request #31 · nf-core/epitopeprediction · GitHub
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Adjust for mouse alleles #31

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Merged
merged 3 commits into from
Aug 25, 2020
Merged

Adjust for mouse alleles #31

merged 3 commits into from
Aug 25, 2020

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skrakau
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@skrakau skrakau commented Mar 19, 2020

Mouse allele names do not contain "*", which is used to access the allele results. I added "H-2-" to this.

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skrakau commented Mar 23, 2020

Does currently not work when running pipeline on variants, due to missing reference. Make sure only run in combination with peptides (or later proteins).

@christopher-mohr christopher-mohr added the enhancement New feature or request label Mar 25, 2020
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Blocked by changes necessary in FRED2 for now.

@skrakau skrakau force-pushed the adjust_for_mousealleles branch from 6c7bc07 to 24d8565 Compare April 1, 2020 13:01
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skrakau commented Apr 1, 2020

If a mouse allele is provided and --input is specified, it will complain and exit. However, it is a bit suboptimal, we should check in general supported models and alleles.

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skrakau commented Apr 23, 2020

However, it is a bit suboptimal, we should check in general supported models and alleles.

this will be addressed in #44.

However, we should add a test for mouse alleles.

@skrakau skrakau force-pushed the adjust_for_mousealleles branch from a60acce to 337007a Compare April 30, 2020 16:19
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skrakau commented Apr 30, 2020

:D so all tests run through even though the (only) mouse allele in the test is not supported yet in the current Fred2 version 2.0.6, the results will be empty.

This should still wait for a new FRED release

(with FRED-2/Fred2#242 and/or #44 this would not happen again)

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New FRED2 release finally there: https://github.com/FRED-2/Fred2/releases/tag/v2.0.7

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christopher-mohr reviewed Aug 7, 2020
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@christopher-mohr christopher-mohr merged commit 8410e9d into nf-core:dev Aug 25, 2020
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