Prot multisample

Processing unimodal multi-sample ADT data.

Info

ID: prot_multisample
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_multisample/main.nf \
  --help

Run command

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

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

# QC metrics calculation options
top_n_vars: [50, 100, 200, 500]

# 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_multisample/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 concatenated file string, required, example: "concatenated"
--input Path to the samples. file, required, example: "dataset.h5mu"

Outputs

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

QC metrics calculation options

Name Description Attributes
--top_n_vars Number of top vars to be used to calculate cumulative proportions. If not specified, proportions are not calculated. --top_n_vars 20,50 finds cumulative proportion to the 20th and 50th most expressed vars. List of integer, default: 50, 100, 200, 500, multiple_sep: ","

Authors

  • Dries Schaumont (author)

Visualisation

flowchart LR
    p0(Input)
    p3(toSortedList)
    p5(flatMap)
    p7(toSortedList)
    p9(Output)
    p15(clr)
    p17(join)
    p25(prot_calculate_qc_metrics)
    p27(join)
    p34(Output)
    p0-->p3
    p3-->p5
    p5-->p7
    p7-->p9
    p5-->p17
    p5-->p15
    p15-->p17
    p17-->p27
    p17-->p25
    p25-->p27
    p27-->p34