qbic-pipelines metapep issues

qbic-pipelines / metapep

From metagenomes to epitopes and beyond

MIT License

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issues

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Change pipeline version

#73 AntoniaSchuster closed 2 years ago
0
Allow efficient parsing of one microbiome_path for multiple microbiome_ids

#72 AntoniaSchuster closed 2 years ago
0
Adjust dockerhub container handling

#71 skrakau opened 3 years ago
0
Allow efficient parsing of one `microbiome_path` for multiple `microbiome_ids`

#70 skrakau closed 1 year ago
1
Weights for type `bins`

#69 skrakau opened 3 years ago
0
Port to DSL2

#68 skrakau closed 2 years ago
0
Pre-filter peptides prior prediction

#67 skrakau opened 3 years ago
0
Fix subsampling option

#66 skrakau opened 3 years ago
0
'list index out of range' error in 'download_proteins' process

#65 skrakau opened 3 years ago
0
Add process to collects some stats

#64 skrakau closed 3 years ago
1
Re-add support for 'proteins' input type

#63 lkuchenb opened 3 years ago
0
Fix caching of buffered chunks using 'toSortedList()'

#62 skrakau closed 3 years ago
0
Rename 'depths' column to 'weights'

#61 lkuchenb closed 3 years ago
0
Add option for `bins` input type - extend data model by entities

#60 skrakau closed 3 years ago
2
Handle score distribution plotting for big data

#59 skrakau closed 3 years ago
0
Include bin or taxa (entity) information - extend data model

#58 skrakau closed 3 years ago
0
Collect and output some stats

#57 skrakau closed 3 years ago
1
Adjust mem requirements for merging and plotting

#56 skrakau closed 3 years ago
0
Revert "Fix argument list size error for high number of chunks"

#55 lkuchenb closed 3 years ago
0
Fix argument list size error for high number of chunks

#54 lkuchenb closed 3 years ago
1
Add extra step to buffer predictions

#53 skrakau closed 3 years ago
1
sbatch error due to too many input files

#52 skrakau closed 3 years ago
0
Add weights and score threshold for plotting

#51 skrakau closed 3 years ago
0
Increase time for `generate_peptides`

#50 skrakau closed 3 years ago
0
Handle caching issues

#49 skrakau closed 3 years ago
1
Changed cache to 'lenient' for some crucial processes

#48 skrakau closed 3 years ago
1
Add peptides subsampling parameter `sample_n`

#47 skrakau closed 3 years ago
0
Parallele `predict_proteins`

#46 skrakau opened 3 years ago
0
Reduce memory footprint of gen_prediction_chunks.py and add progress bar

#45 lkuchenb closed 3 years ago
1
Adjust requested resources

#44 skrakau closed 3 years ago
2
Add params to summary

#43 skrakau closed 3 years ago
0
[FIX] Remove trailing asterisks produced by prodigal

#42 lkuchenb closed 3 years ago
0
Allow 'assembly' input without weights

#41 skrakau closed 3 years ago
0
Changelog fixes

#40 lkuchenb closed 3 years ago
0
Use proteins weights for comparison of prediction scores

#39 skrakau closed 3 years ago
1
Switch SYFPEITHI scores to normalized scores

#38 lkuchenb closed 3 years ago
0
Move epytope / FRED-2 installation to Dockerfile to avoid linting error

#37 lkuchenb closed 3 years ago
0
Add plotting of pediction score distributions

#36 skrakau closed 3 years ago
0
Added smaller assembly for test

#35 skrakau closed 3 years ago
0
Add assembly only test

#34 skrakau closed 3 years ago
0
Clean up channel names

#33 skrakau closed 3 years ago
2
Separate MHC-I and MHC-II integration

#32 lkuchenb opened 3 years ago
0
Add test input file, test profile and ci test for mouse alleles

#31 skrakau closed 3 years ago
0
Renamed testdata files - fix

#30 skrakau closed 3 years ago
0
Renamed testdata files

#29 skrakau closed 3 years ago
0
Update test `input.tsv` and add `test_tiny` profile for developing

#28 skrakau closed 3 years ago
0
Add testdata for `assembly` input

#27 skrakau closed 3 years ago
0
Adjust peptide output formats to data model

#26 skrakau closed 3 years ago
0
Refactor `update_protein_ids.py`

#25 skrakau closed 3 years ago
1
Add new test data

#24 skrakau closed 3 years ago
0