modules/cellrangerarc_count

Module to use Cell Ranger’s ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command.

aligncountreference

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

Description

Module to use Cell Ranger’s ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command.

Input

name:type

description

pattern

`meta`
`:map`

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

`sample_type`
`:string`

The type of sample

`sub_sample`
`:string`

The name of sub sample

`reads`
`:file`

FASTQ files produced using Cell Ranger ARC

*.fastq.gz

`meta2`
`:map`

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

`reference`
`:directory`

Directory containing all the reference indices needed by Cell Ranger ARC

Output

name:type

description

pattern

`outs`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}/outs/**`
`:file`

Files containing the outputs of Cell Ranger ARC

${prefix}/outs/*

`lib`

`meta`
`:map`

Groovy Map containing sample information

`${prefix}_lib.csv`
`:file`

Library

${prefix}_lib.csv

`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 is a set of analysis pipelines that process Chromium Single Cell ARC data.

support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc

modules/cellrangerarc_count

Description

Input

`meta`
`:map`

`sample_type`
`:string`

`sub_sample`
`:string`

`reads`
`:file`

`meta2`
`:map`

`reference`
`:directory`

Output

`outs`

`meta`
`:map`

`${prefix}/outs/**`
`:file`

`lib`

`meta`
`:map`

`${prefix}_lib.csv`
`: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

included in

maintainers

get in touch

modules/cellrangerarc_count

Description

Input

meta:map

sample_type:string

sub_sample:string

reads:file

meta2:map

reference:directory

Output

outs

meta:map

${prefix}/outs/**:file

lib

meta:map

${prefix}_lib.csv: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

included in

maintainers

get in touch

`meta`
`:map`

`sample_type`
`:string`

`sub_sample`
`:string`

`reads`
`:file`

`meta2`
`:map`

`reference`
`:directory`

`outs`

`meta`
`:map`

`${prefix}/outs/**`
`:file`

`lib`

`meta`
`:map`

`${prefix}_lib.csv`
`: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