Prot multisample

Processing unimodal multi-sample ADT data.

Info

ID: prot_multisample
Namespace: multiomics

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 0.12.0 -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
# var_qc_metrics: ["ercc", "highly_variable"]
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 0.12.0 -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
--var_qc_metrics	Keys to select a boolean (containing only True or False) column from .var. For each cell, calculate the proportion of total values for genes which are labeled ‘True’, compared to the total sum of the values for all genes. Defaults to the value from –var_name_mitochondrial_genes.	List of string, example: "ercc,highly_variable", multiple_sep: ","
--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
    v0(Input)
    v3(toSortedList)
    v5(flatMap)
    v6(toSortedList)
    v8(Output)
    v14(clr)
    v16(join)
    v22(filter)
    v28(grep_annotation_column)
    v30(join)
    v34(mix)
    v33(filter)
    v40(calculate_qc_metrics)
    v42(join)
    v50(publish)
    v52(join)
    v58(Output)
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