mapping/cellranger_atac_count
Description
Align fastq files using Cell Ranger ATAC count.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required multiple | The fastq.gz files to align. Can also be a single directory containing fastq.gz files. |
--reference | file required | The path to Cell Ranger reference tar.gz file. Can also be a directory. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | The folder to store the alignment results. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--description | string | Sample description to embed in output files |
--force_cells | integer | Define the top N barcodes with the most fragments overlapping peaks as cells and override the cell calling algorithm. N must be a positive integer <= 20,000. Use this option if the number of cells estimated by Cell Ranger ATAC is not consistent with the barcode rank plot |
--peaks | file | Override peak caller: specify peaks to use in downstream analyses from supplied 3-column BED file. The supplied peaks file must be sorted by position and not contain overlapping peaks; comment lines beginning with # are allowed |
--dim_reduce | string | Dimensionality reduction mode for clustering |
--subsample_rate | double | Downsample to preserve this fraction of reads |
--lanes | string multiple | bcl2fastq option. Semicolon-delimited series of lanes to demultiplex. Use this if you have a sample sheet for an entire flow cell but only want to generate a few lanes for further 10x Genomics analysis. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output./path/to/output"
dim_reduce: [ "lsa" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.0.3 \
-main-script target/nextflow/mapping/cellranger_atac_count/main.nf \
-params-file params.yaml Relationships
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Current component
mapping/cellranger_atac_countopenpipeline v4.0.3
Uses
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