Cell Ranger mapping

A pipeline for running Cell Ranger mapping.

Info

ID: cellranger_mapping
Namespace: ingestion

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 0.10.0 -latest \
  -main-script ./workflows/ingestion/cellranger_mapping/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: ["sample_S1_L001_R1_001.fastq.gz", "sample_S1_L001_R2_001.fastq.gz"]
reference: # please fill in - example: "reference.tar.gz"

# Outputs
# output_raw: "$id.$key.output_raw.output_raw"
# output_h5mu: "$id.$key.output_h5mu.h5mu"
obsm_metrics: "metrics_summary"
output_type: "raw"

# Cell Ranger arguments
# expect_cells: 3000
chemistry: "auto"
secondary_analysis: false
generate_bam: true
include_introns: true

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 0.10.0 -latest \
  -profile docker \
  -main-script ./workflows/ingestion/cellranger_mapping/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name	Description	Attributes
--id	ID of the sample.	string, required, example: "foo"
--input	The fastq.gz files to align. Can also be a single directory containing fastq.gz files.	List of file, required, example: "sample_S1_L001_R1_001.fastq.gz", "sample_S1_L001_R2_001.fastq.gz", multiple_sep: ";"
--reference	The path to Cell Ranger reference tar.gz file.	file, required, example: "reference.tar.gz"

Outputs

Name	Description	Attributes
--output_raw	Location where the output folder from Cell Ranger will be stored.	file, required, example: "output_dir"
--output_h5mu	The output from Cell Ranger, converted to h5mu.	file, required, example: "output.h5mu"
--obsm_metrics	Name of the .obsm slot under which to QC metrics (if any).	string, default: "metrics_summary"
--output_type	Which Cell Ranger output to use for converting to h5mu.	string, default: "raw"

Cell Ranger arguments

Name	Description	Attributes
--expect_cells	Expected number of recovered cells, used as input to cell calling algorithm.	integer, example: 3000
--chemistry	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.	string, default: "auto"
--secondary_analysis	Whether or not to run the secondary analysis e.g. clustering.	boolean, default: FALSE
--generate_bam	Whether to generate a BAM file.	boolean, default: TRUE
--include_introns	Include intronic reads in count (default=true unless –target-panel is specified in which case default=false)	boolean, default: TRUE

Authors

• Angela Oliveira Pisco (author)

• Robrecht Cannoodt (author, maintainer)

• Dries De Maeyer (author)

Visualisation

flowchart LR
    p0(Input)
    p2(toSortedList)
    p4(flatMap)
    p11(cellranger_count)
    p13(join)
    p20(cellranger_count_split)
    p22(join)
    p30(from_10xh5_to_h5mu)
    p32(join)
    p39(Output)
    p0-->p2
    p2-->p4
    p4-->p13
    p4-->p11
    p11-->p13
    p13-->p22
    p13-->p20
    p20-->p22
    p22-->p32
    p22-->p30
    p30-->p32
    p32-->p39