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hubmapconsortium / codex-pipeline

CODEX data processing code
GNU General Public License v3.0
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codex-pipeline with singularity #34

Open asom opened 2 years ago

asom commented 2 years ago

When I am trying to run the pipeline with the singularity option: cwltool --singularity pipeline.cwl subm.yaml

I got the following error:

ERROR [job collect_dataset_info] Job error: ("Error collecting output for parameter 'pipeline_config':\nsteps/illumination_first_stitching/collect_dataset_info.cwl:26:7: Did not find output file with glob pattern: '['pipelineConfig.json']'", {}) WARNING [job collect_dataset_info] completed permanentFail ERROR [step collect_dataset_info] Output is missing expected field file:///path_to_pipeline/illumination_first_stitching.cwl#collect_dataset_info/pipeline_config WARNING [step collect_dataset_info] completed permanentFail INFO [workflow illumination_first_stitching] completed permanentFail WARNING [step illumination_first_stitching] completed permanentFail INFO [workflow ] completed permanentFail { "data_json": null, "experiment_config": null, "pipeline_config": null, "stitched_images": null } WARNING Final process status is permanentFail

Any idea how to solve this?