Prot multisample

Processing unimodal multi-sample ADT data.

Info

ID: prot_multisample
Namespace: workflows/prot

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 2.1.1 -latest \
  -main-script target/nextflow/workflows/prot/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"
# layer: "foo"

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

# QC metrics calculation options
# var_qc_metrics: ["ercc,highly_variable"]
top_n_vars: [50, 100, 200, 500]
output_obs_num_nonzero_vars: "num_nonzero_vars"
output_obs_total_counts_vars: "total_counts"
output_var_num_nonzero_obs: "num_nonzero_obs"
output_var_total_counts_obs: "total_counts"
output_var_obs_mean: "obs_mean"
output_var_pct_dropout: "pct_dropout"

# CLR arguments
clr_axis: 0

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/prot/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"`
`--layer`	Input layer to use. If not specified, .X is used.	`string`

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: `","`
`--output_obs_num_nonzero_vars`	Name of column in .obs describing, for each observation, the number of stored values (including explicit zeroes). In other words, the name of the column that counts for each row the number of columns that contain data.	`string`, default: `"num_nonzero_vars"`
`--output_obs_total_counts_vars`	Name of the column for .obs describing, for each observation (row), the sum of the stored values in the columns.	`string`, default: `"total_counts"`
`--output_var_num_nonzero_obs`	Name of column describing, for each feature, the number of stored values (including explicit zeroes). In other words, the name of the column that counts for each column the number of rows that contain data.	`string`, default: `"num_nonzero_obs"`
`--output_var_total_counts_obs`	Name of the column in .var describing, for each feature (column), the sum of the stored values in the rows.	`string`, default: `"total_counts"`
`--output_var_obs_mean`	Name of the column in .obs providing the mean of the values in each row.	`string`, default: `"obs_mean"`
`--output_var_pct_dropout`	Name of the column in .obs providing for each feature the percentage of observations the feature does not appear on (i.e. is missing). Same as `--output_var_num_nonzero_obs` but percentage based.	`string`, default: `"pct_dropout"`

CLR arguments

Name	Description	Attributes
`--clr_axis`	Axis across which CLR is performed.	`integer`, default: `0`

Authors

Dries Schaumont (author)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v2(filter)
    v10(filter)
    v18(clr)
    v25(cross)
    v35(cross)
    v41(filter)
    v164(concat)
    v53(branch)
    v80(concat)
    v65(cross)
    v75(cross)
    v84(branch)
    v111(concat)
    v96(cross)
    v106(cross)
    v112(filter)
    v142(concat)
    v127(cross)
    v137(cross)
    v149(cross)
    v159(cross)
    v171(cross)
    v178(cross)
    v190(cross)
    v197(cross)
    v201(Output)
    subgraph group_prot_qc [prot_qc]
        v58(grep_mitochondrial_genes)
        v89(grep_ribosomal_genes)
        v120(calculate_qc_metrics)
    end
    v53-->v80
    v84-->v111
    v111-->v112
    v0-->v2
    v2-->v10
    v10-->v18
    v18-->v25
    v10-->v25
    v10-->v35
    v53-->v58
    v58-->v65
    v53-->v65
    v53-->v75
    v75-->v80
    v84-->v89
    v89-->v96
    v84-->v96
    v84-->v106
    v106-->v111
    v112-->v120
    v120-->v127
    v112-->v127
    v112-->v137
    v137-->v142
    v142-->v149
    v41-->v149
    v41-->v159
    v159-->v164
    v164-->v171
    v2-->v171
    v171-->v178
    v2-->v178
    v2-->v190
    v190-->v197
    v2-->v197
    v197-->v201
    v35-->v41
    v18-->v35
    v41-->v53
    v58-->v75
    v80-->v84
    v89-->v106
    v120-->v137
    v142-->v159
    v164-->v190
    style group_prot_qc fill:#F0F0F0,stroke:#969696;
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v2 fill:#e3dcea,stroke:#7a4baa;
    style v10 fill:#e3dcea,stroke:#7a4baa;
    style v18 fill:#e3dcea,stroke:#7a4baa;
    style v25 fill:#e3dcea,stroke:#7a4baa;
    style v35 fill:#e3dcea,stroke:#7a4baa;
    style v41 fill:#e3dcea,stroke:#7a4baa;
    style v164 fill:#e3dcea,stroke:#7a4baa;
    style v53 fill:#e3dcea,stroke:#7a4baa;
    style v80 fill:#e3dcea,stroke:#7a4baa;
    style v58 fill:#e3dcea,stroke:#7a4baa;
    style v65 fill:#e3dcea,stroke:#7a4baa;
    style v75 fill:#e3dcea,stroke:#7a4baa;
    style v84 fill:#e3dcea,stroke:#7a4baa;
    style v111 fill:#e3dcea,stroke:#7a4baa;
    style v89 fill:#e3dcea,stroke:#7a4baa;
    style v96 fill:#e3dcea,stroke:#7a4baa;
    style v106 fill:#e3dcea,stroke:#7a4baa;
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