Description

Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command.

Input

name:type
description
pattern

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

csv:file

Sample sheet

*.csv

bcl:file

Base call files

*.bcl.bgzf

Output

name:type
description
pattern

fastq

meta:file

Unaligned FastQ files

*.fastq.gz

*_outs/outs/fastq_path/**/*.fastq.gz:file

Unaligned FastQ files

*.fastq.gz

undetermined_fastq

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_outs/outs/fastq_path/Undetermined*.fastq.gz:file

Undetermined FastQ files

Undetermined*.fastq.gz

reports

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_outs/outs/fastq_path/Reports:directory

Reports

Reports

stats

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_outs/outs/fastq_path/Stats:directory

Stats

Stats

interop

meta:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*_outs/outs/interop_path/*.bin:file

InterOp files

*.bin

versions

versions.yml:file

File containing software version

versions.yml

Tools

cellranger
10X Genomics EULA

Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more.

support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov
demultiplex
Github user ggabernet
Github user edmundmiller
Github user RHReynolds
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