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Merge pull request #795 from hubmapconsortium/pennycuda/codex-pipelin…
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…e-v2.5

Bump codex-pipeline submodule to v2.5
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@sunset666
sunset666 authored Dec 3, 2023
2 parents b1b0937 + b309a20 commit 0c28714
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion src/ingest-pipeline/airflow/dags/cwl/codex-pipeline
Submodule codex-pipeline updated 32 files
+2 −2 .pre-commit-config.yaml
+1 −1 Dockerfile
+51 −12 bin/background_subtraction/run_background_subtraction.py
+0 −1 bin/best_focus/best_z_paths.py
+1 −1 bin/best_focus/file_manipulation.py
+0 −1 bin/codex_stitching/bigstitcher_dataset_meta.py
+2 −0 bin/codex_stitching/image_stitching.py
+0 −3 bin/codex_stitching/secondary_stitcher/mask_stitching.py
+12 −8 bin/codex_stitching/secondary_stitcher/secondary_stitcher.py
+0 −1 bin/codex_stitching/secondary_stitcher/secondary_stitcher_runner.py
+174 −31 bin/convert_to_ometiff.py
+4 −4 bin/create_cytokit_config.py
+1 −4 bin/dataset_info/collect_dataset_info.py
+16 −19 bin/dataset_info/collect_dataset_info_old.py
+6 −1 bin/illumination_correction/run_illumination_correction.py
+0 −4 bin/slicing/slicer.py
+0 −1 bin/utils.py
+0 −4 cytokit-docker/setup_data_directory.py
+1 −1 environment.yml
+4 −2 pipeline-manifest.json
+2 −0 pipeline.cwl
+1 −1 steps/illumination_first_stitching/best_focus.cwl
+1 −1 steps/illumination_first_stitching/collect_dataset_info.cwl
+1 −1 steps/illumination_first_stitching/create_yaml_config.cwl
+1 −1 steps/illumination_first_stitching/first_stitching.cwl
+1 −1 steps/illumination_first_stitching/illumination_correction.cwl
+1 −1 steps/illumination_first_stitching/slicing.cwl
+10 −0 steps/ometiff_second_stitching.cwl
+7 −1 steps/ometiff_second_stitching/background_subtraction.cwl
+7 −2 steps/ometiff_second_stitching/ome_tiff_creation.cwl
+1 −1 steps/ometiff_second_stitching/second_stitching.cwl
+1 −1 steps/run_cytokit.cwl

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