workflows/ingestion/cellranger_mapping

Description

A pipeline for running Cell Ranger mapping.

Type

nextflow_script

License

MIT

Links

Repository

Contributors

Launch

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

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.

Name

Type & Properties

--id

string

required

--input

file

required

multiple

--reference

file

required

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.

Name

Type & Properties

--output_raw

file

required

output

--output_h5mu

file

required

output

--uns_metrics

string

--output_type

string

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)

Name

Type & Properties

--expect_cells

integer

--chemistry

string

--secondary_analysis

boolean

--generate_bam

boolean

--include_introns

boolean