Prot singlesample

Processing unimodal single-sample CITE-seq data.

Info

ID: prot_singlesample
Namespace: multiomics

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 0.12.6 -latest \
  -main-script ./workflows/multiomics/prot_singlesample/main.nf \
  --help

Run command

Example of params.yaml
# Input
id: # please fill in - example: "foo"
input: # please fill in - example: "dataset.h5mu"

# Output
# output: "$id.$key.output.h5mu"

# Filtering options
# min_counts: 200
# max_counts: 5000000
# min_proteins_per_cell: 200
# max_proteins_per_cell: 1500000
# min_cells_per_protein: 3

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script ./workflows/multiomics/prot_singlesample/main.nf \
  -params-file params.yaml
Note

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

Argument groups

Input

Name Description Attributes
--id ID of the sample. string, required, example: "foo"
--input Path to the sample. file, required, example: "dataset.h5mu"

Output

Name Description Attributes
--output Destination path to the output. file, required, example: "output.h5mu"

Filtering options

Name Description Attributes
--min_counts Minimum number of counts captured per cell. integer, example: 200
--max_counts Maximum number of counts captured per cell. integer, example: 5000000
--min_proteins_per_cell Minimum of non-zero values per cell. integer, example: 200
--max_proteins_per_cell Maximum of non-zero values per cell. integer, example: 1500000
--min_cells_per_protein Minimum of non-zero values per gene. integer, example: 3

Authors

  • Dries De Maeyer (author)

  • Robrecht Cannoodt (author, maintainer)

  • Dries Schaumont (author)

Visualisation

flowchart LR
    v0(Input)
    v3(toSortedList)
    v5(flatMap)
    v10(filter)
    v16(grep_annotation_column)
    v18(join)
    v22(mix)
    v21(filter)
    v28(calculate_qc_metrics)
    v30(join)
    v38(publish)
    v40(join)
    v49(filter_with_counts)
    v51(join)
    v59(do_filter)
    v61(join)
    v65(toSortedList)
    v67(Output)
    v21-->v22
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