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 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 |
--uns_metrics | string | Name of the .uns slot under which to QC metrics (if any). |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied. |
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 v4.2.0 \
-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 v4.2.0
Uses
0 relationships
No component dependencies found.