Cell Ranger post-processing

Post-processing Cell Ranger datasets.

Info

ID: cellranger_postprocessing
Namespace: workflows/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 2.1.0 -latest \
  -main-script target/nextflow/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"

# 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"

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/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 TB
    v0(Channel.fromList)
    v2(filter)
    v14(branch)
    v41(concat)
    v19(cellbender_remove_background)
    v26(cross)
    v36(cross)
    v45(branch)
    v72(concat)
    v50(filter_with_counts)
    v57(cross)
    v67(cross)
    v79(cross)
    v86(cross)
    v98(cross)
    v105(cross)
    v109(Output)
    v14-->v41
    v45-->v72
    v0-->v2
    v14-->v19
    v19-->v26
    v14-->v26
    v14-->v36
    v36-->v41
    v45-->v50
    v50-->v57
    v45-->v57
    v45-->v67
    v67-->v72
    v72-->v79
    v2-->v79
    v79-->v86
    v2-->v86
    v2-->v98
    v98-->v105
    v2-->v105
    v105-->v109
    v2-->v14
    v19-->v36
    v41-->v45
    v50-->v67
    v72-->v98
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v14 fill:#e3dcea,stroke:#7a4baa;
    style v41 fill:#e3dcea,stroke:#7a4baa;
    style v19 fill:#e3dcea,stroke:#7a4baa;
    style v26 fill:#e3dcea,stroke:#7a4baa;
    style v36 fill:#e3dcea,stroke:#7a4baa;
    style v45 fill:#e3dcea,stroke:#7a4baa;
    style v72 fill:#e3dcea,stroke:#7a4baa;
    style v50 fill:#e3dcea,stroke:#7a4baa;
    style v57 fill:#e3dcea,stroke:#7a4baa;
    style v67 fill:#e3dcea,stroke:#7a4baa;
    style v79 fill:#e3dcea,stroke:#7a4baa;
    style v86 fill:#e3dcea,stroke:#7a4baa;
    style v98 fill:#e3dcea,stroke:#7a4baa;
    style v105 fill:#e3dcea,stroke:#7a4baa;
    style v109 fill:#e3dcea,stroke:#7a4baa;