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

Description

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

Name (Type)

Description

Pattern

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

]

Path to a 3-column CSV file declaring FASTQ paths, sample names and library types of input ATAC and GEX FASTQs.

Directory containing all the reference indices needed by Cell Ranger ARC

Name (Type)

Description

Pattern

Files containing the outputs of Cell Ranger ARC

${meta.id}/outs/*

File containing software version

versions.yml

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