workflows/generate_qc_report

Description

Run the ingestion QC report generation

Type

nextflow_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
max_samples_per_report: [ 20 ]  
var_name_mitochondrial_genes: [ "mitochondrial" ]  
var_name_ribosomal_genes: [ "ribosomal" ]  
min_total_counts: [ 10 ]  
min_num_nonzero_vars: [ 10 ]  
run_cellbender: [ false ]  
cellbender_epochs: [ 150 ]  
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" ]  
output_qc_report: "$id.$key.output_qc_report._*.html"  
output_processed_h5mu: "$id.$key.output_processed_h5mu"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_qc.git \  
  -revision v0.2.2 \  
  -main-script target/nextflow/workflows/generate_qc_report/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string	The sample IDs to include in the report. If not provided, the sample IDs will be extracted from the h5mu files.
--input	file required	The input h5mu files.
--ingestion_method	string required
--sample_metadata	file	The sample metadata file corresponding to .obs fields in the h5mu input files, to be used for grouping in the report.
--max_samples_per_report	integer	The maximum number of samples to be included per report. Multiple reports will be generated (with samples equally divided over all reports) if number of input samples exceeds this threshold.

Name

Type & Properties

--id

string

--input

file

required

--ingestion_method

string

required

--sample_metadata

file

--max_samples_per_report

integer

Options

Name	Type & Properties	Description
--var_gene_names	string	The column name in the .var h5mu files that contains the gene names. If not provided, .var_names will be used.
--obs_metadata	string multiple	The metadata keys in the h5mu .obs to include in the report.

Name

Type & Properties

--var_gene_names

string

--obs_metadata

string

multiple

QC options

Name	Type & Properties	Description
--var_name_mitochondrial_genes	string	In which .var slot to store a boolean array corresponding the mitochondrial genes.
--var_name_ribosomal_genes	string	In which .var slot to store a boolean array corresponding the ribosomal genes.
--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.

Name

Type & Properties

--var_name_mitochondrial_genes

string

--var_name_ribosomal_genes

string

--min_total_counts

integer

--min_num_nonzero_vars

integer

Cellbender options

Name	Type & Properties	Description
--run_cellbender	boolean	Whether to run cellbender or not.
--cellbender_epochs	integer	Number of epochs to train cellbender.

Name

Type & Properties

--run_cellbender

boolean

--cellbender_epochs

integer

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

Outputs

Name	Type & Properties	Description
--output_qc_report	file required multiple output	The output HTML report
--output_processed_h5mu	file required output	Folder containing the processed h5mu files.

Name

Type & Properties

--output_qc_report

file

required

multiple

output

--output_processed_h5mu

file

required

output