ingestion_qc/h5mu_to_qc_json

Description

Takes H5MU files that have been ingested by CellRanger, Xenium or CosMx and processed by the QC workflow, and generates:

A JSON file that contains the combined data for the QC report
A JSON file that defines the layout and structure of the QC report

Inputs

Name	Type & Properties	Description
--input	file required multiple	The input h5mu file(s)
--modality	string	The modality to use
--ingestion_method	string required	Method that was used to ingest the data - this will define the structure of the report that is generated.
--obs_sample_id	string	The key in the h5mu file that contains the sample ID. If not provided, each H5MU file will be considered as a separate sample.
--obs_total_counts	string	The key in the h5mu .obs field that contains the total counts.
--obs_num_nonzero_vars	string	The key in the h5mu .obs field that contains the number of nonzero vars.
--obs_fraction_mitochondrial	string	The key in the h5mu .obs field that contains the fraction mitochondrial genes.
--obs_fraction_ribosomal	string	The key in the h5mu .obs field that contains the fraction ribosomal genes.

Name

Type & Properties

--input

file

required

multiple

--modality

string

--ingestion_method

string

required

--obs_sample_id

string

--obs_total_counts

string

--obs_num_nonzero_vars

string

--obs_fraction_mitochondrial

string

--obs_fraction_ribosomal

string

Outputs

Name	Type & Properties	Description
--output	file required output	The output JSON file
--output_reporting_json	file required output	The output JSON file that defines the QC report

Name

Type & Properties

--output

file

required

output

--output_reporting_json

file

required

output

Filtering & grouping options

Name	Type & Properties	Description
--min_total_counts	integer	Minimum total counts for a cell to be included in the output
--min_num_nonzero_vars	integer	Minimum number of nonzero vars for a cell to be included in the output
--obs_metadata	string multiple	The metadata keys in the h5mu .obs to include in the output JSON.

Name

Type & Properties

--min_total_counts

integer

--min_num_nonzero_vars

integer

--obs_metadata

string

multiple

Options for CellRanger reports

Name	Type & Properties	Description
--obs_cellbender	string multiple	The cellbender keys in the h5mu .obs to include in the output JSON
--uns_cellranger_metrics	string	The key in the h5mu file .uns that contains the cellranger metrics

Name

Type & Properties

--obs_cellbender

string

multiple

--uns_cellranger_metrics

string

Options for Xenium reports

Name	Type & Properties	Description
--obs_nucleus_area	string	The key in the h5mu .obs field that contains the nucleus area.
--obs_cell_area	string	The key in the h5mu .obs field that contains the cell area.
--obs_x_coord	string	The key in the h5mu .obs field that contains the x coordinate.
--obs_y_coord	string	The key in the h5mu .obs field that contains the y coordinate.
--obs_control_probe_counts	string	The key in the h5mu .obs field that contains the number of control probes.
--obs_control_codeword_counts	string	The key in the h5mu .obs field that contains the number of control codewords.

Name

Type & Properties

--obs_nucleus_area

string

--obs_cell_area

string

--obs_x_coord

string

--obs_y_coord

string

--obs_control_probe_counts

string

--obs_control_codeword_counts

string

Options for CosMx reports

Name	Type & Properties	Description
--obs_area	string	The key in the h5mu .obs field that contains the cell area.
--obs_aspect_ratio	string	The key in the h5mu .obs field that contains the aspect ratio.
--obs_dapi_stain	string multiple	The keys in the h5mu .obs field that contains the DAPI stain intensity.
--obs_membrane_stain	string multiple	The keys in the h5mu .obs field that contains the membrane stain intensity.
--obs_panck_stain	string multiple	The keys in the h5mu .obs field that contains the PanCK stain intensity.
--obs_cd45_stain	string multiple	The keys in the h5mu .obs field that contains the CD45 stain intensity.
--obs_cd3_stain	string multiple	The keys in the h5mu .obs field that contains the CD3 stain intensity.

Name

Type & Properties

--obs_area

string

--obs_aspect_ratio

string

--obs_dapi_stain

string

multiple

--obs_membrane_stain

string

multiple

--obs_panck_stain

string

multiple

--obs_cd45_stain

string

multiple

--obs_cd3_stain

string

multiple

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
obs_sample_id: [ "sample_id" ]  
obs_total_counts: [ "total_counts" ]  
obs_num_nonzero_vars: [ "num_nonzero_vars" ]  
obs_fraction_mitochondrial: [ "fraction_mitochondrial" ]  
obs_fraction_ribosomal: [ "fraction_ribosomal" ]  
output: "$id.$key.output.json"  
output_reporting_json: "$id.$key.output_reporting_json.json"  
min_total_counts: [ 10 ]  
min_num_nonzero_vars: [ 10 ]  
obs_cellbender:  
  [  
    "cellbender_background_fraction",  
    "cellbender_cell_probability",  
    "cellbender_cell_size",  
    "cellbender_droplet_efficiency"  
  ]  
uns_cellranger_metrics: [ "metrics_cellranger" ]  
obs_nucleus_area: [ "nucleus_area" ]  
obs_cell_area: [ "cell_area" ]  
obs_x_coord: [ "x_coord" ]  
obs_y_coord: [ "y_coord" ]  
obs_control_probe_counts: [ "control_probe_counts" ]  
obs_control_codeword_counts: [ "control_codeword_counts" ]  
obs_area: [ "Area" ]  
obs_aspect_ratio: [ "AspectRatio" ]  
obs_dapi_stain: [ "Mean.DAPI", "Max.DAPI" ]  
obs_membrane_stain: [ "Mean.MembraneStain", "Max.MembraneStain" ]  
obs_panck_stain: [ "Mean.PanCK", "Max.PanCK" ]  
obs_cd45_stain: [ "Mean.CD45", "Max.CD45" ]  
obs_cd3_stain: [ "Mean.CD3", "Max.CD3" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_qc.git \  
  -revision v0.2.1 \  
  -main-script target/nextflow/ingestion_qc/h5mu_to_qc_json/main.nf \  
  -params-file params.yaml

ingestion_qc/h5mu_to_qc_json

Inputs

Outputs

Filtering & grouping options

Options for CellRanger reports

Options for Xenium reports

Options for CosMx reports

Run this component

Relationships

Used by

Uses