mapping/cellranger_count_split
Description
Split 10x Cell Ranger output directory into separate output fields.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Output directory from a Cell Ranger count run. |
--filtered_h5 | file output | Output path for the h5 file storing the filtered counts. |
--metrics_summary | file output | Where to store the 'metrics_summary' CSV file. |
--molecule_info | file output | Where to store Cell Ranger's 'molecule_info.h5' file. |
--bam | file output | Location of output BAM files. |
--bai | file output | Where to store the BAM index files. |
--raw_h5 | file output | Output path for the h5 file storing the raw counts. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
filtered_h5: "$id.$key.filtered_h5.h5"
metrics_summary: "$id.$key.metrics_summary.csv"
molecule_info: "$id.$key.molecule_info.h5"
bam: "$id.$key.bam.bam"
bai: "$id.$key.bai.bai"
raw_h5: "$id.$key.raw_h5.h5"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.2.0 \
-main-script target/nextflow/mapping/cellranger_count_split/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
mapping/cellranger_count_splitopenpipeline v4.2.0
Uses
0 relationships
No component dependencies found.