modules/cellranger_mkfastq

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

referencemkfastqfastqilluminabcl2fastq

https://github.com/nf-core/modules/[...]/modules/nf-core/cellranger/mkfastq

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`
`:map`

Groovy Map containing sample information

`_outs/outs/fastq_path//_S[0-9]_R?_00?.fastq.gz`
`:file`

Read FastQ files

*_S[0-9]*_R?_00?.fastq.gz

`fastq_idx`

`meta`
`:map`

Groovy Map containing sample information

`_outs/outs/fastq_path//_S[0-9]_I?_00?.fastq.gz`
`:file`

Index FastQ files

*_S[0-9]*_I?_00?.fastq.gz

`undetermined_fastq`

`meta`
`:map`

Groovy Map containing sample information

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

Undetermined FastQ files

Undetermined*.fastq.gz

`reports`

`meta`
`:map`

Groovy Map containing sample information

`*_outs/outs/fastq_path/Reports`
`:directory`

Reports

Reports

`stats`

`meta`
`:map`

Groovy Map containing sample information

`*_outs/outs/fastq_path/Stats`
`:directory`

Stats

Stats

`interop`

`meta`
`:map`

Groovy Map containing sample information

`_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