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.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input folder. Must contain the output from a cellranger multi run. |
--output -o | file output | Output h5mu file. |
--output_compression | string | |
--uns_metrics | string | Name of the .uns slot under which to QC metrics (if any). |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output.h5mu"
uns_metrics: [ "metrics_cellranger" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision 1.0.4 \
-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
convert/from_cellranger_multi_to_h5muopenpipeline 1.0.4
Uses
0 relationships
No component dependencies found.