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Annotation workflow #829

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Changelog

... Describe your changes ...

Issue ticket number and link

Closes #xxxx (Replace xxxx with the GitHub issue number)

Checklist before requesting a review

  • I have performed a self-review of my code

  • Conforms to the Contributor's guide

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Documentation
    • Bug fixes

  • Proposed changes are described in the CHANGELOG.md

  • CI tests succeed!

VladimirShitov and others added 30 commits March 25, 2024 11:35
@VladimirShitov
Add ATAC demux (#726)
9ccc4a3
@DriesSchaumont
Remove muon as test dependency for concatenate_h5mu. (#773)
41b60be
@dorien-er @DriesSchaumont
scGPT binning component (#765)
7ec3ba4 
Co-authored-by: Dries Schaumont <[email protected]>
@jakubmajercik @DriesSchaumont
Cellranger Multi: output stdout/err on when cellranger failed (#766)
a169145 
* stdout/err stored on fail

Co-authored-by: Dries Schaumont <[email protected]>

* changelog entry added + minor fixes

---------

Co-authored-by: Dries Schaumont <[email protected]>
@jakubmajercik @DriesSchaumont
Implement cellranger mkgtf (#771)
0cae088 
* cellranger mkgtf component working and tested

* removed comments

* changelog entry added

* test unique attribute in result

* multiple attribute par added

* removed unused packages

* use pytest, multiple attributes tested

---------

Co-authored-by: DriesSchaumont <[email protected]>
@DriesSchaumont
Merge remote-tracking branch 'origin/main' into develop
39dedf2
@DriesSchaumont
Update 10x and Illumina related components. (#774)
0489f1d 
* CI - Build: Fix second occurance of namespace separator

* Update 10x and Illumina related components.

* Add tests for fixed RNA

* Remove -k option for pytest

* Undo accidental removal of resource

* Trigger ci

* Increase memory a bit

* Increase timeout a little bit

* Update CHANGELOG
@dorien-er
Add no-lane-splitting parameter to BCL Convert (#804)
3eebd2b 
* add no-lane-splitting param

* add no-lane-splitting param

* add more unit tests

* update changelog

* remove unused file

* fix typo changelog

* undo blank line
@dorien-er
pynndescent_knn component
512b600
@dorien-er
add split_samples component
2aae946
@dorien-er
add reference subworkflow
431bf52
@dorien-er
add process_samples subworkflow
885d395
@dorien-er
combine reference and query channel
9510a79
@dorien-er
processing subworkflows combined
0d2b37e
@dorien-er
processing subworkflows
0df61c9
@dorien-er
update split samples component to drop na columns
f7e3394
@dorien-er
add harmony knn annotation subworkflow
2150846
@dorien-er
annotation workflow with knn harmony
a7825a2
@dorien-er
add merge in to aaas branch
edf1c09
@dorien-er
update config pynndescent_knn
1b3a9db
@dorien-er
update config pynndescent_knn
63bb1e3
@dorien-er
update config pynndescent_knn
b912b8c
@dorien-er
update config pynndescent_knn
d78314f
@dorien-er
update config pynndescent_knn
939b743
@dorien-er
update config pynndescent_knn
a5cc5a9
@dorien-er
updata annotation script with label mapper
1eef53e
@dorien-er
update pynndescent_knn config
76dac69
@dorien-er
update pynndescent_knn config
9b03c8c
@dorien-er
update pynndescent_knn config
468aa3c
@dorien-er
update pynndescent_knn config
1ba3f4f
@dorien-er
update unit tests
5231a32
@dorien-er
update integration test
26e74c6
@dorien-er
update pynndescent_knn
b4be058
@dorien-er
add common params and utilities
95e1c9c
@dorien-er
update resources test script to have finetuned model available
df8c48d
@dorien-er
celltype annotation workflow
9a774e8
@dorien-er
add scgpt annotation to aaas
fb33343
@dorien-er
remove niceview
2df9773
@dorien-er
update memory requirements nextflow
a77cef4
@dorien-er
update harmony_knn
f285eb8
@dorien-er
add integration subworkflow files
ab49288
@dorien-er
update annotation component
7c68b03
@dorien-er
update scgpt annotation workflow
0f8ffae
@dorien-er
update service workflow
d589571
@dorien-er
update harmony_knn workflow
8bc1cd1
@dorien-er
update scgpt leiden workflow and create scgpt knn subworkflow
dd4ff89
@dorien-er
update scgpt leiden workflow and create scgpt knn subworkflow
06ed76f
@dorien-er
add authors
98cb4f9
@dorien-er
generalize scgpt params
9deaeef
@dorien-er
undo scgpt general arguments
9155ba0
@dorien-er
add rename_var component
8c74661
@dorien-er
fix unit tests
b34d309
@dorien-er
add scgpt integration knn to service
ba125c1
@dorien-er
update rename_var
519b3ca
@dorien-er
bug fix binning
3ae8d4a
@dorien-er
bug fix binning
aaaa950
@dorien-er
add viash build to integration test
76b97d0
@dorien-er
add integration workflow to annotation workflow
86d7398
@dorien-er
Merge remote-tracking branch 'origin/main' into annotation-workflow
838fe1d
@dorien-er
remove outdated files
0486b38
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4 participants
@dorien-er @VladimirShitov @DriesSchaumont @jakubmajercik