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19 Open 57 Closed
19 Open 57 Closed
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Issues list

Implement the logic to draw UMI ditsribution plots enhancement New feature or request steps/calib_dedup calib deduplication step workflow
#118 opened Jun 28, 2024 by nsyzrantsev
Optimize concatenation of output annotations in IgBLAST steps/igblast igblast (cdr3 mapping and annotating) step
#117 opened Jun 26, 2024 by nsyzrantsev
Optimize the IgBLAST step to process target sequence data enhancement New feature or request workflow
#116 opened Jun 26, 2024 by nsyzrantsev
@nsyzrantsev
PyUMI fails with an unreadable error invalid This doesn't seem right steps/pyumi umi preprocessing step
#114 opened Jun 25, 2024 by nsyzrantsev
Create a container to generate an archive with olga models steps/cdr3nt_error_corrector cdr3 error correction step workflow
#100 opened Jun 17, 2024 by nsyzrantsev
Create a container to generate a vidjil reference enhancement New feature or request steps/vidjil vidjil (cdr3 mapping) step workflow
#99 opened Jun 17, 2024 by nsyzrantsev
Reformat pipeline structure priority: low workflow
#85 opened Jun 3, 2024 by nsyzrantsev
3 tasks done
Research: docker container around pyigmap? priority: low workflow
#79 opened May 22, 2024 by nsyzrantsev
Set CPUs count and RAM size as parameters at pyigmap workflow
#65 opened May 14, 2024 by nsyzrantsev
Update python3.9 -> python3.12 priority: low steps/calib_dedup calib deduplication step steps/cdr3nt_error_corrector cdr3 error correction step steps/downloader steps/fastp fastq merging step steps/igblast igblast (cdr3 mapping and annotating) step steps/vidjil vidjil (cdr3 mapping) step
#63 opened May 14, 2024 by nsyzrantsev
6 tasks
Build reference inside docker container priority: medium steps/cdr3nt_error_corrector cdr3 error correction step steps/igblast igblast (cdr3 mapping and annotating) step steps/vidjil vidjil (cdr3 mapping) step
#59 opened May 12, 2024 by nsyzrantsev
1
Skip annotation field if empty in filter_non_productive invalid This doesn't seem right steps/cdr3nt_error_corrector cdr3 error correction step
#56 opened May 12, 2024 by mikessh
Add cell barcode support in pyumi step enhancement New feature or request steps/pyumi umi preprocessing step
#37 opened May 2, 2024 by nsyzrantsev
5 tasks
@yuliajk
Add unit tests to fastp, vidjil and igblast steps/fastp fastq merging step steps/igblast igblast (cdr3 mapping and annotating) step steps/vidjil vidjil (cdr3 mapping) step
#22 opened Apr 18, 2024 by nsyzrantsev
Add pipeline version/build info to json log enhancement New feature or request steps/cdr3nt_error_corrector cdr3 error correction step
#21 opened Apr 17, 2024 by mikessh
Add support of single-end reads enhancement New feature or request steps/calib_dedup calib deduplication step steps/fastp fastq merging step workflow
#17 opened Apr 14, 2024 by nsyzrantsev
Skip empty vidjil output in igblast enhancement New feature or request
#15 opened Apr 14, 2024 by nsyzrantsev
Set new parameters to fastp/vidjil/igblast enhancement New feature or request
#4 opened Apr 5, 2024 by nsyzrantsev
Add support for cell/sample barcodes and demultiplexing logic to calib-dedup step enhancement New feature or request steps/calib_dedup calib deduplication step
#1 opened Apr 5, 2024 by nsyzrantsev
2 of 4 tasks
4
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