modules/cellrangerarc_mkfastq

Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command.

referencemkfastqfastqilluminabcl2fastq

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

Description

Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`bcl`
`:file`

Base call files

*.bcl.bgzf

`csv`
`:file`

Sample sheet

*.csv

Output

name:type

description

pattern

`fastq`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`${prefix}/outs/fastq_path/*.fastq.gz`
`:file`

Unaligned FastQ files

${prefix}/outs/fastq_path/*.fastq.gz

`versions_cellrangerarc`

`${task.process}`
`:string`

The name of the process

`cellrangerarc`
`:string`

The name of the tool

`cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`cellrangerarc`
`:string`

The name of the tool

`cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'`
`:eval`

The expression to obtain the version of the tool

Tools

cellrangerarc
10x Genomics EULA

Cell Ranger Arc 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-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

modules/cellrangerarc_mkfastq

Description

Input

`meta`
`:map`

`bcl`
`:file`

`csv`
`:file`

Output

`fastq`

`meta`
`:map`

`${prefix}/outs/fastq_path/*.fastq.gz`
`:file`

`versions_cellrangerarc`

`${task.process}`
`:string`

`cellrangerarc`
`:string`

`cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`cellrangerarc`
`:string`

`cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'`
`:eval`

Tools

cellrangerarc
10x Genomics EULA

maintainers

get in touch

modules/cellrangerarc_mkfastq

Description

Input

meta:map

bcl:file

csv:file

Output

fastq

meta:map

${prefix}/outs/fastq_path/*.fastq.gz:file

versions_cellrangerarc

${task.process}:string

cellrangerarc:string

cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//':eval

Topics

versions

${task.process}:string

cellrangerarc:string

cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//':eval

Tools

cellrangerarc 10x Genomics EULA

maintainers

get in touch

`meta`
`:map`

`bcl`
`:file`

`csv`
`:file`

`fastq`

`meta`
`:map`

`${prefix}/outs/fastq_path/*.fastq.gz`
`:file`

`versions_cellrangerarc`

`${task.process}`
`:string`

`cellrangerarc`
`:string`

`cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'`
`:eval`

`versions`

`${task.process}`
`:string`

`cellrangerarc`
`:string`

`cellranger-arc --version 2>&1 | sed 's/cellranger-arc cellranger-arc-//'`
`:eval`

cellrangerarc
10x Genomics EULA