Cellranger atac count

Align fastq files using Cell Ranger ATAC count.

Info

ID: cellranger_atac_count
Namespace: mapping

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -main-script target/nextflow/mapping/cellranger_atac_count/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
input: # please fill in - example: ["sample_S1_L001_R1_001.fastq.gz", "sample_S1_L001_R2_001.fastq.gz"]
reference: # please fill in - example: "reference.tar.gz"

# Outputs
# output: "$id.$key.output"

# Arguments
description: ""
# force_cells: 123
# peaks: "path/to/file"
dim_reduce: "lsa"
# subsample_rate: 0.1
# lanes: ["1,3"]

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/mapping/cellranger_atac_count/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name	Description	Attributes
--input	The fastq.gz files to align. Can also be a single directory containing fastq.gz files.	List of file, required, example: "sample_S1_L001_R1_001.fastq.gz", "sample_S1_L001_R2_001.fastq.gz", multiple_sep: ";"
--reference	The path to Cell Ranger reference tar.gz file. Can also be a directory.	file, required, example: "reference.tar.gz"

Outputs

Name	Description	Attributes
--output	The folder to store the alignment results.	file, required, example: "/path/to/output"

Arguments

Name	Description	Attributes
--description	Sample description to embed in output files	string, default: ""
--force_cells	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	integer
--peaks	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	file
--dim_reduce	Dimensionality reduction mode for clustering	string, default: "lsa"
--subsample_rate	Downsample to preserve this fraction of reads	double, example: 0.1
--lanes	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.	List of string, example: "1,3", multiple_sep: ";"

Authors

• Vladimir Shitov (author)