mapping/cellranger_atac_count

Description

Align fastq files using Cell Ranger ATAC count.

Type

bash_script

License

MIT

Links

Repository

Contributors

Launch

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

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.

Name

Type & Properties

--input

file

required

multiple

--reference

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	The folder to store the alignment results.

Name

Type & Properties

--output

file

required

output

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.

Name

Type & Properties

--description

string

--force_cells

integer

--peaks

file

--dim_reduce

string

--subsample_rate

double

--lanes

string

multiple