demux/cellranger_atac_mkfastq
Description
Demultiplex raw sequencing data for ATAC experiments
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 |
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 Relationships
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Current component
demux/cellranger_atac_mkfastqopenpipeline v4.2.0
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