demux/cellranger_atac_mkfastq

Description

Demultiplex raw sequencing data for ATAC experiments

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'  
barcode_mismatches: [ 1 ]  
output: "$id.$key.output./path/to/output"  
reports: "$id.$key.reports.reports_dir"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/demux/cellranger_atac_mkfastq/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input	file required	Path of Illumina BCL run folder.
--csv	file required	The path to the simple layout sample sheet.
--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.
--use_bases_mask	string multiple	bcl2fastq option. Use to clip extra bases off a read if you ran extra cycles for QC.
--delete_undetermined	boolean_true	bcl2fastq option. Delete the Undetermined FASTQs generated by bcl2fastq. Useful if you are demultiplexing a small number of samples from a large flow cell.
--barcode_mismatches	integer	bcl2fastq option. Use this option to change the number of allowed mismatches per index adapter (0, 1, 2).
--output	file required output	The folder to store the demux results
--reports	file output	Reports directory

Name

Type & Properties

--input

file

required

--csv

file

required

--lanes

string

multiple

--use_bases_mask

string

multiple

--delete_undetermined

boolean_true

--barcode_mismatches

integer

--output

file

required

output

--reports

file

output