1- openpipeline
1+ OpenPipeline
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44<!-- README.md is generated by running 'quarto render README.qmd' -->
@@ -23,39 +23,37 @@ The results below were generated by running
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26- | Namespace | Component | Tests | Maintainer | Duration (s) |
27- | :--------------| :------------------------------------------------------------------------------| :------------------------------------------------------------------------------| :----------------------------------------| -------------:|
28- | bcl_demux | [ cellranger_mkfastq] ( src/bcl_demux/cellranger_mkfastq/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-SETUP%20FAIL!-red.png ) | [ rcannood] ( https://github.com/rcannood ) | 0 |
29- | cluster | [ leiden] ( src/cluster/leiden/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 391 |
30- | convert | [ from_10xh5_to_h5ad] ( src/convert/from_10xh5_to_h5ad/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 339 |
31- | convert | [ from_10xh5_to_h5mu] ( src/convert/from_10xh5_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 381 |
32- | convert | [ from_10xmtx_to_h5mu] ( src/convert/from_10xmtx_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 375 |
33- | convert | [ from_bdrhap_to_h5ad] ( src/convert/from_bdrhap_to_h5ad/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 380 |
34- | convert | [ from_csv_to_h5mu] ( src/convert/from_csv_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | Dries De Maeyer | 44 |
35- | convert | [ from_h5ad_to_h5mu] ( src/convert/from_h5ad_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 344 |
36- | convert | [ from_h5mu_to_seurat] ( src/convert/from_h5mu_to_seurat/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-0%20out%20of%201-red.png ) | [ rcannood] ( https://github.com/rcannood ) | 349 |
37- | demux | [ cellranger_mkfastq] ( src/demux/cellranger_mkfastq/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 375 |
38- | dimred | [ pca] ( src/dimred/pca/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 393 |
39- | dimred | [ umap] ( src/dimred/umap/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 375 |
40- | download | [ download_file] ( src/download/download_file/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 303 |
41- | download | [ sync_test_resources] ( src/download/sync_test_resources/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 317 |
42- | filter | [ do_filter] ( src/filter/do_filter/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 392 |
43- | filter | [ filter_with_counts] ( src/filter/filter_with_counts/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 379 |
44- | filter | [ filter_with_hvg] ( src/filter/filter_with_hvg/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 380 |
45- | filter | [ filter_with_scrublet] ( src/filter/filter_with_scrublet/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 392 |
46- | interactive | [ run_cellxgene] ( src/interactive/run_cellxgene/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | | 42 |
47- | interactive | [ run_cirrocumulus] ( src/interactive/run_cirrocumulus/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | | 47 |
48- | mapping | [ bd_rhapsody_wta] ( src/mapping/bd_rhapsody_wta/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-DNF-red.png ) | [ rcannood] ( https://github.com/rcannood ) | NA |
49- | mapping | [ bd_rhapsody_wta_1\_ 10] ( src/mapping/bd_rhapsody_wta_1_10/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-0%20out%20of%201-red.png ) | [ rcannood] ( https://github.com/rcannood ) | 394 |
50- | mapping | [ bd_rhapsody_wta_1\_ 10_1] ( src/mapping/bd_rhapsody_wta_1_10_1/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-0%20out%20of%201-red.png ) | [ rcannood] ( https://github.com/rcannood ) | 391 |
51- | mapping | [ cellranger_count] ( src/mapping/cellranger_count/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 407 |
52- | mapping | [ cellranger_count_split] ( src/mapping/cellranger_count_split/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | [ rcannood] ( https://github.com/rcannood ) | 42 |
53- | neighbors | [ find_neighbors] ( src/neighbors/find_neighbors/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 376 |
54- | process_10xh5 | [ filter_10xh5] ( src/process_10xh5/filter_10xh5/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 391 |
55- | report | [ mermaid] ( src/report/mermaid/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 339 |
56- | transfer | [ publish] ( src/transfer/publish/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Toni Verbeiren | 303 |
57- | transform | [ log1p] ( src/transform/log1p/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 391 |
58- | transform | [ normalize_total] ( src/transform/normalize_total/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | Dries De Maeyer | 375 |
59- | transform | [ regress_out] ( src/transform/regress_out/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 391 |
26+ | Namespace | Component | Tests | Maintainer | Duration (s) |
27+ | :--------------| :-----------------------------------------------------------------------------| :------------------------------------------------------------------------------| :----------------------------------------| -------------:|
28+ | bcl_demux | [ cellranger_mkfastq] ( NA ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | | 54 |
29+ | cluster | [ leiden] ( src/cluster/leiden/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 316 |
30+ | convert | [ from_10xh5_to_h5ad] ( src/convert/from_10xh5_to_h5ad/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 120 |
31+ | convert | [ from_10xh5_to_h5mu] ( src/convert/from_10xh5_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 371 |
32+ | convert | [ from_10xmtx_to_h5mu] ( src/convert/from_10xmtx_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 370 |
33+ | convert | [ from_bdrhap_to_h5ad] ( src/convert/from_bdrhap_to_h5ad/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 306 |
34+ | convert | [ from_csv_to_h5mu] ( src/convert/from_csv_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | Dries De Maeyer | 76 |
35+ | convert | [ from_h5ad_to_h5mu] ( src/convert/from_h5ad_to_h5mu/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 133 |
36+ | convert | [ from_h5mu_to_seurat] ( src/convert/from_h5mu_to_seurat/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 109 |
37+ | demux | [ cellranger_mkfastq] ( src/demux/cellranger_mkfastq/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 88 |
38+ | dimred | [ pca] ( src/dimred/pca/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 349 |
39+ | dimred | [ umap] ( src/dimred/umap/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 349 |
40+ | download | [ download_file] ( src/download/download_file/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 99 |
41+ | download | [ sync_test_resources] ( src/download/sync_test_resources/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 89 |
42+ | filter | [ do_filter] ( src/filter/do_filter/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 140 |
43+ | filter | [ filter_with_counts] ( src/filter/filter_with_counts/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 384 |
44+ | filter | [ filter_with_hvg] ( src/filter/filter_with_hvg/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 124 |
45+ | filter | [ filter_with_scrublet] ( src/filter/filter_with_scrublet/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 365 |
46+ | interactive | [ run_cellxgene] ( src/interactive/run_cellxgene/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | | 0 |
47+ | interactive | [ run_cirrocumulus] ( src/interactive/run_cirrocumulus/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | | 0 |
48+ | mapping | [ bd_rhapsody_wta] ( src/mapping/bd_rhapsody_wta/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 943 |
49+ | mapping | [ cellranger_count] ( src/mapping/cellranger_count/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-1%20out%20of%201-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 194 |
50+ | mapping | [ cellranger_count_split] ( src/mapping/cellranger_count_split/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-no%20tests-orange.png ) | [ rcannood] ( https://github.com/rcannood ) | 0 |
51+ | neighbors | [ find_neighbors] ( src/neighbors/find_neighbors/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 155 |
52+ | process_10xh5 | [ filter_10xh5] ( src/process_10xh5/filter_10xh5/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 120 |
53+ | report | [ mermaid] ( src/report/mermaid/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 261 |
54+ | transfer | [ publish] ( src/transfer/publish/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Toni Verbeiren | 68 |
55+ | transform | [ log1p] ( src/transform/log1p/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 345 |
56+ | transform | [ normalize_total] ( src/transform/normalize_total/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | Dries De Maeyer | 120 |
57+ | transform | [ regress_out] ( src/transform/regress_out/config.vsh.yaml ) | ![ tests] ( https://img.shields.io/badge/tests-2%20out%20of%202-brightgreen.png ) | [ rcannood] ( https://github.com/rcannood ) | 276 |
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