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General: Initial changes to add addt'l metadata to the dag provenance… #979

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General: Initial changes to add addt'l metadata to the dag provenance… #979

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… list

Juan Puerto added 26 commits November 19, 2024 14:30
General: Initial changes to add addt'l metadata to the dag provenance…
4b4e86f 
… list
General: Fixes for initial dag prov support
864a9c2
General: Fixes for initial dag prov support
d03758b
General: Update pas_ftu_segmentation
5fab8e8
General: Make sure to set workflow_version and description
258747e
General: Switch to using YAML parsing
5c5604a
General: Use task_ids
7cc811a
General: Use task_ids
92dfde1
General: Define new function to build cwl command rather than writing…
ea6b774 
… the same code block multiple times
Utils: Fix param specification and pipeline_version getting using YAML
11b6c00
Utils: Only set the value if there is something to actually set. Alwa…
b61ff27 
…ys set --outdir. Add support for additional cwl_parameters. Add support for param values that are of type list.
OmeTiff Pyramid: Slight clean up
f30b1c9
PAS FTU Segmentation: Slight clean up
8d2d347
Bulk ATACseq: Convert to new workflows format
4c78c6b
CellDIVE: Convert to new workflows format
e648bd3
CODEX: Convert to new workflows format
04dc0e9
DeepCell: Update to use new workflows format
cb7f9d8
Multiome: Update to use new workflows format
4736b5e
Multiome: Formatting
b2d37c3
DAGs: Add workflow_version and description. pass it to function to up…
779e80a 
…date dag provenance list
DAGs: Update ometiff_pyramid_ims.py to use new cwl_workflows structure
1d116ff
DAGs: Update phenocycler_deepcell.py to use new cwl_workflows structure
b2ddbbc
DAGs: Update salmon_rnaseq.py to use new cwl_workflows structure
a6b39a3
DAGs: Update salmon_rnaseq_bulk.py to use new cwl_workflows structure
abb9a4b
DAGs: Update sc_atac_seq.py to use new cwl_workflows structure
83eb965
DAGs: Update visium.py to use new cwl_workflows structure
fad32d3
@jpuerto-psc jpuerto-psc marked this pull request as ready for review November 25, 2024 19:19
gesinaphillips
gesinaphillips approved these changes Nov 25, 2024
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I did my best to double check things!

src/ingest-pipeline/airflow/dags/pas_ftu_segmentation.py Show resolved Hide resolved
@jpuerto-psc jpuerto-psc requested a review from sunset666 December 2, 2024 20:58
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@sunset666 - realizing now that I forgot to make changes for the EPIC seg mask DAG. Just made those changes so we will have to re-merge/update.

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@gesinaphillips gesinaphillips gesinaphillips approved these changes

@sunset666 sunset666 sunset666 approved these changes

@jswelling jswelling Awaiting requested review from jswelling jswelling is a code owner

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@jpuerto-psc @sunset666 @gesinaphillips