inputs.json

{
  "spatial_geomx_analysis.projects": "Array[WomCompositeType {\n slides -> Array[WomCompositeType {\n asap_slide_id -> String\ngeomx_lab_annotation_xlsx -> File\nsamples -> Array[WomCompositeType {\n fastq_I1s -> Array[File]\nfastq_R1s -> Array[File]+\nsample_id -> String\nbatch -> String?\nfastq_I2s -> Array[File]\nfastq_R2s -> Array[File]+ \n}] \n}]\ngeomx_config_ini -> File\nrun_project_cohort_analysis -> Boolean\nraw_data_bucket -> String\nasap_team_id -> String\nasap_dataset_id -> String\nasap_project_sample_metadata_csv -> File\nstaging_data_buckets -> Array[String]\nasap_dataset_doi_url -> String \n}]",
  "spatial_geomx_analysis.geomxngs_config_pkc": "File",
  "spatial_geomx_analysis.min_segment_reads": "Int (optional, default = 1000)",
  "spatial_geomx_analysis.min_percent_reads_trimmed": "Int (optional, default = 80)",
  "spatial_geomx_analysis.min_percent_reads_stitched": "Int (optional, default = 80)",
  "spatial_geomx_analysis.min_percent_reads_aligned": "Int (optional, default = 80)",
  "spatial_geomx_analysis.min_saturation": "Int (optional, default = 50)",
  "spatial_geomx_analysis.min_neg_ctrl_count": "Int (optional, default = 1)",
  "spatial_geomx_analysis.max_ntc_count": "Int (optional, default = 1000)",
  "spatial_geomx_analysis.min_nuclei": "Int (optional, default = 100)",
  "spatial_geomx_analysis.min_segment_area": "Int (optional, default = 5000)",
  "spatial_geomx_analysis.cell_type_markers_list": "File",
  "spatial_geomx_analysis.min_genes_detected_in_percent_segment": "Float (optional, default = 0.01)",
  "spatial_geomx_analysis.n_top_genes": "Int (optional, default = 3000)",
  "spatial_geomx_analysis.n_comps": "Int (optional, default = 30)",
  "spatial_geomx_analysis.batch_key": "String (optional, default = \"batch_id\")",
  "spatial_geomx_analysis.leiden_resolution": "Float (optional, default = 0.4)",
  "spatial_geomx_analysis.container_registry": "String",
  "spatial_geomx_analysis.zones": "String (optional, default = \"us-central1-c us-central1-f\")"
}