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openpipelines-bio
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openpipeline
https://openpipelines.bio
MIT License
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Generate scGPT cross_check_genes module
#747
dorien-er
opened
1 month ago
0
CI - Build: Fix second occurance of namespace separator
#746
DriesSchaumont
closed
1 month ago
0
Fix retag for viash-hub not using correct namespace separator
#745
DriesSchaumont
closed
1 month ago
0
Remove unused CI step and improve input checks.
#744
DriesSchaumont
closed
1 month ago
0
rna_singlesample: fix 'obs_name_mitochondrial_fraction'
#743
DriesSchaumont
closed
1 month ago
0
Add t-SNE component
#742
jakubmajercik
closed
1 month ago
1
Release 1.0.0-rc2
#741
DriesSchaumont
closed
1 month ago
0
Fix --output arguments in workflows
#740
DriesSchaumont
closed
1 month ago
1
Add densMAP component
#739
jakubmajercik
opened
1 month ago
0
TODO list for the paper
#738
VladimirShitov
opened
1 month ago
1
Add t-SNE component
#737
jakubmajercik
closed
1 month ago
0
Update nextflow resource labels for cellbender
#736
DriesSchaumont
closed
1 month ago
0
Update tests prebuilt asserters
#735
jakubmajercik
closed
1 month ago
0
Update tests for components under multiomics/process_samples
#734
jakubmajercik
closed
1 month ago
0
Add scaling to workflows.
#733
DriesSchaumont
opened
1 month ago
0
Revert "Cellranger multi: better test for absolute path"
#732
DriesSchaumont
closed
1 month ago
0
grep_annotation_column: fix fractions for sparse input data /w low bitsize dtypes
#731
DriesSchaumont
closed
1 month ago
0
dataflow/merge all tests refactored and working in pytest - error in …
#730
jakubmajercik
closed
1 month ago
0
Output the cellranger log when the cellranger multi process exited with a non-zero exitcode.
#729
DriesSchaumont
closed
1 month ago
0
grep_annotation_column: fix calculating fraction for observation with 0 counts.
#728
DriesSchaumont
closed
1 month ago
0
Cellranger multi: better test for absolute path
#727
DriesSchaumont
closed
1 month ago
0
Feature/atac demux
#726
VladimirShitov
closed
1 month ago
1
Build(deps): Bump nf-core/setup-nextflow from 1.5.2 to 2.0.0
#725
dependabot[bot]
closed
1 month ago
0
mock par added
#724
jakubmajercik
closed
1 month ago
0
Update metadata join csv test
#723
jakubmajercik
closed
1 month ago
0
Update from h5mu to h5ad tests
#722
jakubmajercik
closed
1 month ago
0
1.0.0rc1: fraction mitochondrial genes columns is not correctly passed to component
#721
DriesSchaumont
closed
1 month ago
0
Update metadata join csv test
#720
jakubmajercik
closed
2 months ago
0
Update from h5mu to h5ad tests
#719
jakubmajercik
closed
1 month ago
0
metadata_grep_annotation_column is failing in the integrationt tests with `Fractions are not within bounds`
#718
DriesSchaumont
closed
1 month ago
0
Cellranger Multi: fix relative input path for vdj_inner_enrichment_primers
#717
DriesSchaumont
closed
2 months ago
0
[BUG] Path of inner enrichment primers is not converted to absolute path for processing
#716
ddemaeyer
closed
2 months ago
0
Add scaling component as an optional component to the pipeline
#715
ddemaeyer
opened
2 months ago
0
split_modalities: add logging, remove duplicate argument and update tests.
#714
DriesSchaumont
closed
2 months ago
0
Fix double quotes in component descriptions
#713
DriesSchaumont
closed
2 months ago
0
Change namespace separator for OpenPipelines v1
#712
rcannood
closed
1 month ago
0
Check error messages after closing the `pytest.raises` context manager blocks
#711
DriesSchaumont
closed
2 months ago
0
CI: Do checks on error messages after closing the context manager blocks.
#710
DriesSchaumont
closed
2 months ago
0
Update scarches component
#709
VladimirShitov
opened
2 months ago
0
process_samples: fix combining state when merging.
#708
DriesSchaumont
closed
2 months ago
0
Continuation of #700: Change multiple_sep to ';'
#707
DriesSchaumont
closed
2 months ago
0
Bump viash to 0.8.4
#706
DriesSchaumont
closed
2 months ago
0
Updated read_percentage function for cellranger multi metrics processing #704
#705
LucHendriks
closed
2 months ago
0
Bug in processing of metrics summary file after cellranger multi
#704
LucHendriks
closed
2 months ago
0
add scanpy score_genes and score_genes_cell_cycle components
#703
dorien-er
closed
2 months ago
0
Add possibility to specify raw data layer in process_samples pipeline.
#702
DriesSchaumont
closed
2 months ago
0
Dataset nxf schema
#701
dorien-er
closed
2 months ago
0
Change separator for arguments with multiple input from `:` to `;`
#700
rcannood
closed
2 months ago
1
Pin jax,jaxlib for scvi-tools
#699
DriesSchaumont
closed
2 months ago
0
Bump nf-core/setup-nextflow from 1.5.1 to 1.5.2
#698
dependabot[bot]
closed
2 months ago
0
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