reference/build_cellranger_arc_reference

Description

Build a Cell Ranger-arc and -atac compatible reference folder from user-supplied genome FASTA and gene GTF files. Creates a new folder named after the genome.

Type

bash_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
non_nuclear_contigs: [ "chrM" ]  
output: "$id.$key.output.cellranger_reference"  
genome: [ "output" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.1 \  
  -main-script target/nextflow/reference/build_cellranger_arc_reference/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--genome_fasta	file required	Reference genome fasta.
--annotation_gtf	file required	Reference annotation.
--motifs_file	file	Transcription factor motifs in JASPAR format. See https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/advanced/references
--non_nuclear_contigs	string multiple	Name(s) of contig(s) that do not have any chromatin structure, for example, mitochondria or plastids. These contigs are excluded from peak calling since the entire contig will be "open" due to a lack of chromatin structure. Leave empty if there are no such contigs.
--output	file required output	Output folder
--genome	string required	Name of the genome. This will be the name of the intermediate output folder
--organism	string	Name of the organism. This is displayed in the web summary but is otherwise not used in the analysis.
--subset_regex	string	Will subset the reference chromosomes using the given regex.

Name

Type & Properties

--genome_fasta

file

required

--annotation_gtf

file

required

--motifs_file

file

--non_nuclear_contigs

string

multiple

--output

file

required

output

--genome

string

required

--organism

string

--subset_regex

string