workflows/prot/prot_multisample

Description

Processing unimodal multi-sample ADT data.

Type

nextflow_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
output: "$id.$key.output.h5mu"  
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_axis: [ 0 ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 2.0.0 \  
  -main-script target/nextflow/workflows/prot/prot_multisample/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--id	string required	ID of the concatenated file
--input	file required	Path to the samples.
--layer	string	Input layer to use. If not specified, .X is used.

Name

Type & Properties

--id

string

required

--input

file

required

--layer

string

Outputs

Name	Type & Properties	Description
--output	file required output	Destination path to the output.

Name

Type & Properties

--output

file

required

output

QC metrics calculation options

Name	Type & Properties	Description
--var_qc_metrics	string multiple	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.
--top_n_vars	integer multiple	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.
--output_obs_num_nonzero_vars	string	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.
--output_obs_total_counts_vars	string	Name of the column for .obs describing, for each observation (row), the sum of the stored values in the columns.
--output_var_num_nonzero_obs	string	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.
--output_var_total_counts_obs	string	Name of the column in .var describing, for each feature (column), the sum of the stored values in the rows.
--output_var_obs_mean	string	Name of the column in .obs providing the mean of the values in each row.
--output_var_pct_dropout	string	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.

Name

Type & Properties

--var_qc_metrics

string

multiple

--top_n_vars

integer

multiple

--output_obs_num_nonzero_vars

string

--output_obs_total_counts_vars

string

--output_var_num_nonzero_obs

string

--output_var_total_counts_obs

string

--output_var_obs_mean

string

--output_var_pct_dropout

string

CLR arguments

Name	Type & Properties	Description
--clr_axis	integer	Axis across which CLR is performed.

Name

Type & Properties

--clr_axis

integer