convert/from_cellranger_multi_to_h5mu

Description

Converts the output from cellranger multi to a single .h5mu file.
By default, will map the following library type names to modality names:

Gene Expression: rna
Peaks: atac
Antibody Capture: prot
VDJ: vdj
VDJ-T: vdj_t
VDJ-B: vdj_b
CRISPR Guide Capture: crispr
Multiplexing Capture: hashing

Other library types have their whitepace removed and dashes replaced by
underscores to generate the modality name.

Currently does not allow parsing the output from cell barcode demultiplexing.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output._*.h5mu"  
sample_csv: "$id.$key.sample_csv.csv"  
uns_metrics: [ "metrics_cellranger" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 2.1.2 \  
  -main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input -i	file required	Input folder. Must contain the output from a cellranger multi run.
--output -o	file multiple output	Locations for the output files. Must contain a wildcard (*) character, which will be replaced with the sample name.
--sample_csv	file output	CSV file describing the sample name per output file
--output_compression	string
--uns_metrics	string	Name of the .uns slot under which to QC metrics (if any).

Name

Type & Properties

--input

-i

file

required

--output

-o

file

multiple

output

--sample_csv

file

output

--output_compression

string

--uns_metrics

string