Add 3D IMC segmentation #975
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| *get_cwltool_base_cmd(tmpdir), | ||
| # '--singularity', | ||
| workflow, | ||
| "--gpus=all", |
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the pipeline.cwl doesn't have gpus as an attribute.
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Correct. GPU requirements apply to each individual CommandLineTool in a CWL workflow, not a Workflow that composes them together. The segmentation step has the GPU requirement: https://github.com/hubmapconsortium/imc-3d-segmentation/blob/main/steps/segmentation.cwl#L7
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yes, but it needs to be declared so it can be passed along, currently it throws an error because of that.
usage: /hive/users/hive/hubmap/vm001-dev/ingest-pipeline/src/ingest-pipeline/airflow/dags/cwl/imc-3d-segmentation/pipeline.cwl
[-h] --cytoplasm_markers CYTOPLASM_MARKERS --input_dir INPUT_DIR
--membrane_markers MEMBRANE_MARKERS --nucleus_markers NUCLEUS_MARKERS
[--processes PROCESSES]
[job_order]
.../imc-3d-segmentation/pipeline.cwl: error: unrecognized arguments: --gpus=all
Example pipeline with working argument:
https://github.com/hubmapconsortium/mibi-pipeline/blob/7501938b53db117551ff02ca5597256d6795852e/pipeline.cwl#L8
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Ah, that was my mistake in making a copy of the MIBI DAG and then modifying appropriately -- I'd forgotten that this workflow doesn't accept a --gpus parameter at all. I'll remove it from the DAG as soon as I can.
| "La139" "--nucleus_markers", | ||
| "Ir191" "--input_dir", |
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Probably missing ',' after La139 and Ir191?
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