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Initial Release v1.0.0 #132

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tillenglert
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Dev to Master PR for Initial release 1.0.0!! 🥳

tillenglert and others added 30 commits August 1, 2023 10:07
@tillenglert
update Changelog
a610d08
@tillenglert
software_versions for plot_entity_binding_ratios
aba423c
@tillenglert
Remove headers, unnecessary imports and commented code
6e5d95b
@tillenglert
update changelog
a3663d2
@skrakau
Merge pull request #86 from skrakau/adjust_resources
5630b21 
Adjusted used resource request labels
@tillenglert
Merge pull request #90 from tillenglert/script_headers
33eb79d 
Script headers
@tillenglert
Merge branch 'dev' into bugfix/peptide_lengths
ec2ee2b
@tillenglert
Review comment
3ee1efa
@tillenglert
Merge pull request #89 from tillenglert/bugfix/peptide_lengths
fc14e3f 
Bugfix peptide Lengths and include log instead of tsv
@tillenglert
Add new parameter to
ba29802 
allow all peptide lengths to be predicted
@tillenglert
Include new parameter in process_input
0740fe1
@tillenglert
Additional checks in epytope_predict to circumvent errors
87633e5
@tillenglert
python black
8efd391
@tillenglert
Update Changelog
1f902d6
@tillenglert
Add check for peptide length parameter and replace exit with error
3f4ba65
@tillenglert
Add comment on check
cba996e
@tillenglert
update changelog
81bfb31
@tillenglert
Add test to allow all peptide lengths for mouse test
488ce19
@tillenglert
Change larger mosue test including also taxa to reduce the number of …
e02e13a 
…peptide lengths automatically to test this functionality
@tillenglert
Add test taxa only
3ae3c66
@tillenglert
add test bins only
a88ebc0
@tillenglert
Add tests to gh ci
432c4d3
@tillenglert
Add correct name and remove ncbi from test all peptide lengths
c6ba6ed
@tillenglert
Add test taxa to tests run with gh secrets
e859215
@tillenglert
Add comment to add ncbi mail and pw
119a158
@tillenglert
remove todos in test profile
e1c5c07
@tillenglert
Add tests for mhcflurry and mhcnuggets
39fa300
@tillenglert
Adjust line in usage.md for test not needing any configuration additi…
5d65ada 
…onally added assembly only
@tillenglert
Use mhc2 alleles test for mhcnuggets class 2
b277395
@nf-core-bot
[automated] Fix linting with Prettier
7e65b30
tillenglert and others added 15 commits September 13, 2024 15:34
@tillenglert
Add bugfix from #135 for testing on cfc
4d52218
@tillenglert
Update all tests to include the stats.tsv instead of stats.txt
922682c
@tillenglert
Update all test snapshots
1d998e0
@tillenglert
Merge pull request #135 from tillenglert/bugfix/duplicated_rows_prote…
825420d 
…in_entities

Bugfix: duplicated rows in `protein_entity.tsv`
@tillenglert
Merge branch 'dev' into multiqc_additional_stats
879e41b
@tillenglert
fix multiqc for model info branch
9cf2794
@tillenglert
Change according to suggestion of @skrakau and fix alleles not assign…
2fb5df0 
…ed to condition
@tillenglert
drop prediction_score column
529182c
@tillenglert
code and comment refactorings
1dff437
@tillenglert
Update all snapshots for new stats module
a9a3d8e
@tillenglert
update test bins
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@tillenglert
Licensing
e968570
@tillenglert
Merge pull request #134 from tillenglert/multiqc_additional_stats
68258d0 
MultiQC-Additional overview stat table
@tillenglert
gen_prediction_chunks change to main() and move global var
8391100
@tillenglert
Add verbose error to gen_prediction_chunks
59e7a2c
jonasscheid
jonasscheid approved these changes Oct 1, 2024
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LGTM 🚀 !

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@skrakau skrakau skrakau left review comments

@sateeshperi sateeshperi sateeshperi left review comments

@jonasscheid jonasscheid jonasscheid approved these changes

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@tillenglert @nictru @skrakau @sateeshperi @jonasscheid @nf-core-bot