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; style v112 fill:#e3dcea,stroke:#7a4baa; style v142 fill:#e3dcea,stroke:#7a4baa; style v120 fill:#e3dcea,stroke:#7a4baa; style v127 fill:#e3dcea,stroke:#7a4baa; style v137 fill:#e3dcea,stroke:#7a4baa; style v149 fill:#e3dcea,stroke:#7a4baa; style v159 fill:#e3dcea,stroke:#7a4baa; style v171 fill:#e3dcea,stroke:#7a4baa; style v178 fill:#e3dcea,stroke:#7a4baa; style v190 fill:#e3dcea,stroke:#7a4baa; style v197 fill:#e3dcea,stroke:#7a4baa; style v201 fill:#e3dcea,stroke:#7a4baa;
Prot multisample
Processing unimodal multi-sample ADT data.
Info
ID: prot_multisample
Namespace: workflows/prot
Links
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 2.1.0 -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 2.1.0 -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 |