Cellranger atac mkfastq

Demultiplex raw sequencing data for ATAC experiments

Info

ID: cellranger_atac_mkfastq
Namespace: demux

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/demux/cellranger_atac_mkfastq/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: "/path/to/bcl"
csv: # please fill in - example: "SampleSheet.csv"
# lanes: ["1,3"]
# use_bases_mask: ["y50n,I6n,Y50n"]
delete_undetermined: false
barcode_mismatches: 1
# output: "fastqs"
# reports: "$id.$key.reports"

# 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/demux/cellranger_atac_mkfastq/main.nf \
  -params-file params.yaml
Note

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

Argument group

Arguments

Name Description Attributes
--input Path of Illumina BCL run folder. file, required, example: "/path/to/bcl"
--csv The path to the simple layout sample sheet. file, required, example: "SampleSheet.csv"
--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: ","
--use_bases_mask bcl2fastq option. Use to clip extra bases off a read if you ran extra cycles for QC. List of string, example: "y50n,I6n,Y50n", multiple_sep: ","
--delete_undetermined bcl2fastq option. Delete the Undetermined FASTQs generated by bcl2fastq. Useful if you are demultiplexing a small number of samples from a large flow cell. boolean_true
--barcode_mismatches bcl2fastq option. Use this option to change the number of allowed mismatches per index adapter (0, 1, 2). integer, default: 1
--output The folder to store the demux results file, required, default: "fastqs", example: "/path/to/output"
--reports Reports directory file, example: "reports_dir"

Authors

  • Vladimir Shitov (author)