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.
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. |
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 v4.2.0 \
-main-script target/nextflow/reference/build_cellranger_arc_reference/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
reference/build_cellranger_arc_referenceopenpipeline v4.2.0
Uses
0 relationships
No component dependencies found.