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 0.10.0 -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
# min_fraction_mito: 0
# max_fraction_mito: 0.2

# 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/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
--min_fraction_mito Minimum fraction of proteins that are mitochondrial. double, example: 0
--max_fraction_mito Maximum fraction of proteins that are mitochondrial. double, example: 0.2

Authors

  • Dries De Maeyer (author)

  • Robrecht Cannoodt (author, maintainer)

  • Dries Schaumont (author)

Visualisation

flowchart LR
    p0(Input)
    p3(toSortedList)
    p5(flatMap)
    p12(filter_with_counts)
    p14(join)
    p22(do_filter)
    p24(join)
    p30(toSortedList)
    p32(Output)
    p0-->p3
    p3-->p5
    p5-->p14
    p5-->p12
    p12-->p14
    p14-->p24
    p14-->p22
    p22-->p24
    p24-->p30
    p30-->p32