Cell Ranger post-processing

Post-processing Cell Ranger datasets.

Info

ID: cellranger_postprocessing
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_postprocessing/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
id: # please fill in - example: "foo"
input: # please fill in - example: "input.h5mu"

# Outputs
# output: "$id.$key.output.output"

# Correction arguments
perform_correction: false
cellbender_epochs: 150

# Filtering arguments
# min_genes: 100
# min_counts: 1000

# 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_postprocessing/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	Input h5mu file created by running Cell Ranger and converting its output to h5mu.	file, required, example: "input.h5mu"

Outputs

Name	Description	Attributes
--output	The converted h5mu file.	file

Correction arguments

Name	Description	Attributes
--perform_correction	Whether or not to run CellBender to perform count correction.	boolean_true
--cellbender_epochs	Number of epochs to run CellBender for.	integer, default: 150

Filtering arguments

Name	Description	Attributes
--min_genes	Minimum number of counts required for a cell to pass filtering.	integer, example: 100
--min_counts	Minimum number of genes expressed required for a cell to pass filtering.	integer, example: 1000

Authors

• Angela Oliveira Pisco (author)

• Robrecht Cannoodt (author, maintainer)

Visualisation

flowchart LR
    p0(Input)
    p6(from_10xh5_to_h5mu)
    p8(join)
    p12(toSortedList)
    p14(flatMap)
    p15(filter)
    p21(cellbender_remove_background)
    p23(join)
    p27(mix)
    p26(filter)
    p28(filter)
    p34(filter_with_counts)
    p36(join)
    p40(mix)
    p39(filter)
    p46(publish)
    p48(join)
    p54(Output)
    p14-->p15
    p14-->p26
    p26-->p27
    p27-->p28
    p27-->p39
    p39-->p40
    p0-->p8
    p0-->p6
    p6-->p8
    p8-->p12
    p12-->p14
    p15-->p23
    p15-->p21
    p21-->p23
    p23-->p27
    p28-->p36
    p28-->p34
    p34-->p36
    p36-->p40
    p40-->p48
    p40-->p46
    p46-->p48
    p48-->p54