workflows/gdo/gdo_singlesample
Description
Processing unimodal single-sample guide-derived oligonucleotide (GDO) data.
Input
Name | Type & Properties | Description |
|---|---|---|
--id | string required | ID of the sample. |
--input | file required | Path to the sample. |
--layer | string | Input layer to start from. By default, .X will be used. |
Output
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | Destination path to the output. |
Filtering options
Name | Type & Properties | Description |
|---|---|---|
--min_counts | integer | Minimum number of counts captured per cell. |
--max_counts | integer | Maximum number of counts captured per cell. |
--min_guides_per_cell | integer | Minimum of non-zero values per cell. |
--max_guides_per_cell | integer | Maximum of non-zero values per cell. |
--min_cells_per_guide | integer | Minimum of non-zero values per gene. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
id: "run"
output: "$id.$key.output.h5mu"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.0 \
-main-script target/nextflow/workflows/gdo/gdo_singlesample/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
workflows/gdo/gdo_singlesampleopenpipeline v4.0.0