mapping/cellranger_count
Description
Align fastq files using Cell Ranger count.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required multiple | The fastq.gz files to align. Can also be a single directory containing fastq.gz files. |
--reference | file required | The path to Cell Ranger reference tar.gz file. Can also be a directory. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file required output | The folder to store the alignment results. |
Arguments
Name | Type & Properties | Description |
|---|---|---|
--expect_cells | integer | Expected number of recovered cells, used as input to cell calling algorithm. |
--chemistry | string | Assay configuration. - auto: autodetect mode - threeprime: Single Cell 3' - fiveprime: Single Cell 5' - SC3Pv1: Single Cell 3' v1 - SC3Pv2: Single Cell 3' v2 - SC3Pv3: Single Cell 3' v3 - SC3Pv3LT: Single Cell 3' v3 LT - SC3Pv3HT: Single Cell 3' v3 HT - SC5P-PE: Single Cell 5' paired-end - SC5P-R2: Single Cell 5' R2-only - SC-FB: Single Cell Antibody-only 3' v2 or 5' See https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry- for more information. |
--secondary_analysis | boolean | Whether or not to run the secondary analysis e.g. clustering. |
--generate_bam | boolean | Whether to generate a BAM file. |
--include_introns | boolean | Include intronic reads in count (default=true unless --target-panel is specified in which case default=false) |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output./path/to/output"
chemistry: [ "auto" ]
secondary_analysis: [ false ]
generate_bam: [ true ]
include_introns: [ true ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision 1.0.4 \
-main-script target/nextflow/mapping/cellranger_count/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
mapping/cellranger_countopenpipeline 1.0.4
Uses
0 relationships
No component dependencies found.