workflows/ingestion/cellranger_mapping
Description
A pipeline for running Cell Ranger mapping.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--id | string required | ID of the sample. |
--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. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output_raw | file required output | Location where the output folder from Cell Ranger will be stored. |
--output_h5mu | file required output | The output from Cell Ranger, converted to h5mu. |
--uns_metrics | string | Name of the .uns slot under which to QC metrics (if any). |
--output_type | string | Which Cell Ranger output to use for converting to h5mu. |
Cell Ranger 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'
id: "run"
output_raw: "$id.$key.output_raw.output_dir"
output_h5mu: "$id.$key.output_h5mu.h5mu"
uns_metrics: [ "metrics_summary" ]
output_type: [ "raw" ]
chemistry: [ "auto" ]
secondary_analysis: [ false ]
generate_bam: [ true ]
include_introns: [ true ]
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.2.0 \
-main-script target/nextflow/workflows/ingestion/cellranger_mapping/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
workflows/ingestion/cellranger_mappingopenpipeline v4.2.0