hubmapconsortium · SFD5311 · Jan 7, 2025 · Jan 7, 2025 · Jan 7, 2025 · Jan 9, 2025
@@ -76,12 +76,15 @@
 [submodule "src/ingest-pipeline/airflow/dags/cwl/ribca"]
 	path = src/ingest-pipeline/airflow/dags/cwl/ribca
 	url = https://github.com/hubmapconsortium/ribca
+[submodule "src/ingest-pipeline/airflow/dags/cwl/rna-probes-pipeline"]
+	path = src/ingest-pipeline/airflow/dags/cwl/rna-probes-pipeline
+	url = https://github.com/hubmapconsortium/rna-probes-pipeline
+[submodule "src/ingest-pipeline/airflow/dags/cwl/pan-organ-azimuth-annotate"]
+	path = src/ingest-pipeline/airflow/dags/cwl/pan-organ-azimuth-annotate
+	url = https://github.com/hubmapconsortium/pan-organ-azimuth-annotate
 [submodule "src/ingest-pipeline/airflow/dags/cwl/xenium-pipeline"]
 	path = src/ingest-pipeline/airflow/dags/cwl/xenium-pipeline
 	url = https://github.com/hubmapconsortium/xenium-pipeline
 [submodule "src/ingest-pipeline/airflow/dags/cwl/stellar"]
 	path = src/ingest-pipeline/airflow/dags/cwl/stellar
 	url = https://github.com/hubmapconsortium/stellar
-[submodule "src/ingest-pipeline/airflow/dags/cwl/pan-organ-azimuth-annotate"]
-	path = src/ingest-pipeline/airflow/dags/cwl/pan-organ-azimuth-annotate
-	url = https://github.com/hubmapconsortium/pan-organ-azimuth-annotate
@@ -204,6 +204,14 @@ resource_map:
       - 'task_re': '.*'
         'queue': 'general'
         'threads': 6
+  - 'dag_re': 'rna_with_probes'
+    'preserve_scratch': true
+    'lanes': 2
+    # 'lanes': 12
+    'tasks':
+      - 'task_re': '.*'
+        'queue': 'general'
+        'threads': 6
   - 'dag_re': '.xenium'
     'preserve_scratch': true
     'lanes': 2
+0 −20		bin/azimuth/azimuth_analysis.R
+0 −9		pipeline.cwl
+1 −5		steps/azimuth-annotate.cwl
+1 −1		steps/expr-h5ad-adjust.cwl
+1 −1		steps/extract-rna-secondary-matrix.cwl
+1 −1		steps/write-metadata.cwl
+1 −1		.travis.yml
+37 −0		Dockerfile
+0 −0		Dockerfile_fiji
+0 −1		bin/best_focus/best_z_identification.py
+0 −1		bin/best_focus/best_z_paths.py
+0 −1		bin/best_focus/file_manipulation.py
+0 −1		bin/best_focus/run_best_focus_selection.py
+0 −1		bin/codex_stitching/bigstitcher_dataset_meta.py
+0 −1		bin/codex_stitching/directory_management.py
+0 −1		bin/codex_stitching/generate_bigstitcher_macro.py
+0 −1		bin/codex_stitching/image_stitching.py
+0 −1		bin/codex_stitching/run_stitching.py
+0 −1		bin/codex_stitching/secondary_stitcher/mask_stitching.py
+0 −1		bin/codex_stitching/secondary_stitcher/match_masks.py
+0 −1		bin/codex_stitching/secondary_stitcher/secondary_stitcher.py
+0 −1		bin/codex_stitching/secondary_stitcher/secondary_stitcher_runner.py
+5 −8		bin/convert_to_ometiff.py
+0 −1		bin/create_cytokit_config.py
+1 −21		bin/dataset_info/collect_dataset_info.py
+1 −2		bin/dataset_info/collect_dataset_info_old.py
+0 −1		bin/dataset_info/run_collection.py
+0 −1		bin/illumination_correction/generate_basic_macro.py
+0 −1		bin/illumination_correction/run_illumination_correction.py
+0 −1		bin/pipeline_utils/dataset_listing.py
+0 −1		bin/pipeline_utils/pipeline_config_reader.py
+0 −1		bin/slicing/modify_pipeline_config.py
+0 −1		bin/slicing/run_slicing.py
+0 −1		bin/slicing/slicer.py
+0 −1		bin/utils.py
+0 −0		cytokit-docker/Dockerfile
+0 −0		cytokit-docker/cytokit_wrapper.py
+0 −0		cytokit-docker/setup_data_directory.py
+0 −43		docker/codex_scripts/Dockerfile
+0 −25		docker/codex_scripts/environment.yml
+3 −3		docker_images.txt
+25 −0		environment.yml
+2 −2		requirements-test.txt
+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
+1 −1		steps/ometiff_second_stitching/background_subtraction.cwl
+1 −1		steps/ometiff_second_stitching/ome_tiff_creation.cwl
+1 −1		steps/ometiff_second_stitching/second_stitching.cwl
+1 −1		steps/run_cytokit.cwl
+25 −15		Dockerfile
+1 −1		SectionAligner
+0 −185		bin/crop_input_image.py
+0 −28		bin/utils.py
+27 −0		environment.yml
+6 −17		pipeline.cwl
+0 −21		requirements.txt
+1 −1		steps/collect_dataset_info.cwl
+1 −1		steps/collect_output.cwl
+2 −9		steps/convert_to_bioformats.cwl
+0 −35		steps/crop_input_image.cwl
+1 −1		steps/prepare_segmentation_channels.cwl
+29 −0		steps/run_section_aligner.cwl
+1 −1		steps/run_segmentation.cwl
+1 −1		steps/second_stitching.cwl
+1 −1		steps/slicing.cwl
+1 −1		.github/workflows/workflow.yml
+0 −10		anndata-to-ui-manifest.json
+1 −1		containers/mudata-to-ui/VERSION
+8 −8		containers/mudata-to-ui/context/requirements-freeze.txt
+5 −8		containers/mudata-to-ui/context/requirements.txt
+1 −1		containers/mudata-to-ui/test-output-expected/secondary_analysis.zarr/.zattrs
+1 −1		containers/mudata-to-ui/test-output-expected/secondary_analysis.zarr/mod/atac_cbg/.zattrs
+1 −1		containers/mudata-to-ui/test-output-expected/secondary_analysis.zarr/mod/rna/.zattrs
+0 −26		containers/object-by-analyte-to-ui/Dockerfile
+0 −17		containers/object-by-analyte-to-ui/README.md
+0 −1		containers/object-by-analyte-to-ui/VERSION
+0 −123		containers/object-by-analyte-to-ui/context/main.py
+0 −88		containers/object-by-analyte-to-ui/context/requirements-freeze.txt
+0 −9		containers/object-by-analyte-to-ui/context/requirements.txt
+0 −188		containers/object-by-analyte-to-ui/create-test-input.py
+0 −137		containers/object-by-analyte-to-ui/test-input-parameters.json
+ −		containers/object-by-analyte-to-ui/test-input/secondary_analysis.h5mu
+ −		containers/object-by-analyte-to-ui/test-output-expected/secondary_analysis.zarr.zip
+0 −1		containers/object-by-analyte-to-ui/test-output-expected/secondary_analysis_metadata.json
+0 −5		mudata-to-ui-manifest.json
+1 −1		mudata-to-ui.cwl
+0 −12		object-by-analyte-to-ui-manifest.json
+0 −19		object-by-analyte-to-ui.cwl
+1 −1		workflows/mudata-to-ui/test-output-expected/mudata-zarr/secondary_analysis.zarr/.zattrs
+1 −1		workflows/mudata-to-ui/test-output-expected/mudata-zarr/secondary_analysis.zarr/mod/atac_cbg/.zattrs
+1 −1		workflows/mudata-to-ui/test-output-expected/mudata-zarr/secondary_analysis.zarr/mod/rna/.zattrs
+0 −1		workflows/object-by-analyte-to-ui/README.md
+ −		workflows/object-by-analyte-to-ui/test-input/secondary_analysis.h5mu
+0 −3		workflows/object-by-analyte-to-ui/test-job.yml
+ −		workflows/object-by-analyte-to-ui/test-output-expected/mudata-zarr/secondary_analysis.zarr.zip
+0 −1		workflows/object-by-analyte-to-ui/test-output-expected/mudata-zarr/secondary_analysis_metadata.json
+6 −3		bin/analysis/read_visium_positions.py
+1 −2		bin/analysis/squidpy_entry_point.py
+1 −1		steps/bulk-salmon-mouse.cwl
+1 −1		steps/bulk-salmon.cwl
+1 −1		steps/compute-qc-metrics.cwl
+1 −1		steps/expression-matrix.cwl
+1 −1		steps/fastqc.cwl
+1 −1		steps/salmon-quantification/adjust-barcodes.cwl
+1 −1		steps/salmon-quantification/alevin-to-anndata.cwl
+1 −1		steps/salmon-quantification/annotate-cells.cwl
+1 −1		steps/salmon-quantification/salmon-mouse.cwl
+1 −1		steps/salmon-quantification/salmon.cwl
+1 −1		steps/salmon-quantification/trim-reads.cwl
+1 −1		steps/scanpy-analysis.cwl
+1 −1		steps/scvelo-analysis.cwl
+1 −1		steps/squidpy-analysis.cwl
+2 −1		bin/analysis/compute_qc_metrics.py
+0 −88		bin/analysis/human_read_removal.py
+0 −17		docker/human_read_removal/Dockerfile
+0 −1		docker/human_read_removal/requirements.txt
+1 −2		docker_images.txt
+1 −1		pipeline-manifest.json
+1 −1		salmon-rnaseq
+1 −1		steps/adjust-barcodes.cwl
+1 −1		steps/compute-qc-metrics.cwl
+0 −26		steps/human-read-removal.cwl
+1 −1		steps/quantification.cwl
+1 −1		steps/trim-reads.cwl