workflows/ingestion/cellranger_multi

Description

A pipeline for running Cell Ranger multi.

Type

nextflow_script

Contributors

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_cellranger" ]  
gex_chemistry: [ "auto" ]  
gex_secondary_analysis: [ false ]  
gex_generate_bam: [ true ]  
gex_include_introns: [ true ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.0 \  
  -main-script target/nextflow/workflows/ingestion/cellranger_multi/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the sample.
--input	file multiple	The fastq.gz files to align. Can also be a single directory containing fastq.gz files.
--gex_reference	file required	Genome refence index built by Cell Ranger mkref.
--vdj_reference	file	VDJ refence index built by Cell Ranger mkref.
--feature_reference	file	Path to the Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes. Required only for Antibody Capture or CRISPR Guide Capture libraries. See https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref for more information.
--vdj_inner_enrichment_primers	file	V(D)J Immune Profiling libraries: if inner enrichment primers other than those provided in the 10x Genomics kits are used, they need to be specified here as a text file with one primer per line.

Name

Type & Properties

--id

string

required

--input

file

multiple

--gex_reference

file

required

--vdj_reference

file

--feature_reference

file

--vdj_inner_enrichment_primers

file

Feature type-specific input files

Name	Type & Properties	Description
--gex_input	file multiple	The FASTQ files to be analyzed for Gene Expression. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--abc_input	file multiple	The FASTQ files to be analyzed for Antibody Capture. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--cgc_input	file multiple	The FASTQ files to be analyzed for CRISPR Guide Capture. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--mux_input	file multiple	The FASTQ files to be analyzed for Multiplexing Capture. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--vdj_input	file multiple	The FASTQ files to be analyzed for VDJ. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--vdj_t_input	file multiple	The FASTQ files to be analyzed for VDJ-T. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--vdj_t_gd_input	file multiple	The FASTQ files to be analyzed for VDJ-T-GD. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--vdj_b_input	file multiple	The FASTQ files to be analyzed for VDJ-B. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`
--agc_input	file multiple	The FASTQ files to be analyzed for Antigen Capture. FASTQ files should conform to the naming conventions of bcl2fastq and mkfastq: `[Sample Name]_S[Sample Index]_L00[Lane Number]_[Read Type]_001.fastq.gz`

Name

Type & Properties

--gex_input

file

multiple

--abc_input

file

multiple

--cgc_input

file

multiple

--mux_input

file

multiple

--vdj_input

file

multiple

--vdj_t_input

file

multiple

--vdj_t_gd_input

file

multiple

--vdj_b_input

file

multiple

--agc_input

file

multiple

Outputs

Name	Type & Properties	Description
--output_raw	file required output	The raw output folder.
--output_h5mu	file required output	The converted h5mu file.
--uns_metrics	string	Name of the .uns slot under which to QC metrics (if any).

Name

Type & Properties

--output_raw

file

required

output

--output_h5mu

file

required

output

--uns_metrics

string

Cell multiplexing parameters

Name	Type & Properties	Description
--cell_multiplex_sample_id	string	A name to identify a multiplexed sample. Must be alphanumeric with hyphens and/or underscores, and less than 64 characters. Required for Cell Multiplexing libraries.
--cell_multiplex_oligo_ids	string	The Cell Multiplexing oligo IDs used to multiplex this sample. If multiple CMOs were used for a sample, separate IDs with a pipe (e.g., CMO301\|CMO302). Required for Cell Multiplexing libraries.
--cell_multiplex_description	string	A description for the sample.

Name

Type & Properties

--cell_multiplex_sample_id

string

--cell_multiplex_oligo_ids

string

--cell_multiplex_description

string

Gene expression arguments

Name	Type & Properties	Description
--gex_expect_cells	integer	Expected number of recovered cells, used as input to cell calling algorithm.
--gex_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.
--gex_secondary_analysis	boolean	Whether or not to run the secondary analysis e.g. clustering.
--gex_generate_bam	boolean	Whether to generate a BAM file.
--gex_include_introns	boolean	Include intronic reads in count (default=true unless --target-panel is specified in which case default=false)

Name

Type & Properties

--gex_expect_cells

integer

--gex_chemistry

string

--gex_secondary_analysis

boolean

--gex_generate_bam

boolean

--gex_include_introns

boolean

Library arguments

Name	Type & Properties	Description
--library_id	string multiple	The Illumina sample name to analyze. This must exactly match the 'Sample Name' part of the FASTQ files specified in the `--input` argument.
--library_type	string multiple	The underlying feature type of the library. Possible values: "Gene Expression", "VDJ", "VDJ-T", "VDJ-B", "Antibody Capture", "CRISPR Guide Capture", "Multiplexing Capture"
--library_subsample	string multiple	Optional. The rate at which reads from the provided FASTQ files are sampled. Must be strictly greater than 0 and less than or equal to 1.
--library_lanes	string multiple	Lanes associated with this sample. Defaults to using all lanes.

Name

Type & Properties

--library_id

string

multiple

--library_type

string

multiple

--library_subsample

string

multiple

--library_lanes

string

multiple