Calculate qc metrics
Info
ID: calculate_qc_metrics
Namespace: qc
Links
The metrics are comparable to what scanpy.pp.calculate_qc_metrics output, although they have slightly different names:
Var metrics (name in this component -> name in scanpy): - pct_dropout -> pct_dropout_by_{expr_type} - num_nonzero_obs -> n_cells_by_{expr_type} - obs_mean -> mean_{expr_type} - total_counts -> total_{expr_type}
Obs metrics: - num_nonzero_vars -> n_genes_by_{expr_type} - pct_{var_qc_metrics} -> pct_{expr_type}{qc_var} - total_counts{var_qc_metrics} -> total_{expr_type}{qc_var} - pct_of_counts_in_top{top_n_vars}vars -> pct{expr_type}in_top{n}{var_type} - total_counts -> total{expr_type}
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 1.0.2 -latest \
-main-script target/nextflow/qc/calculate_qc_metrics/main.nf \
--help
Run command
Example of params.yaml
# Inputs
input: # please fill in - example: "input.h5mu"
modality: "rna"
# layer: "raw_counts"
# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
# Metrics added to .obs
# var_qc_metrics: ["ercc,highly_variable,mitochondrial"]
# var_qc_metrics_fill_na_value: true
# top_n_vars: [123]
output_obs_num_nonzero_vars: "num_nonzero_vars"
output_obs_total_counts_vars: "total_counts"
# Metrics added to .var
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"
# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
-r 1.0.2 -latest \
-profile docker \
-main-script target/nextflow/qc/calculate_qc_metrics/main.nf \
-params-file params.yaml
Replace -profile docker
with -profile podman
or -profile singularity
depending on the desired backend.
Argument groups
Inputs
Name | Description | Attributes |
---|---|---|
--input |
Input h5mu file | file , required, example: "input.h5mu" |
--modality |
string , default: "rna" |
|
--layer |
string , example: "raw_counts" |
Metrics added to .obs
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. | List of string , example: "ercc,highly_variable,mitochondrial" , multiple_sep: ";" |
--var_qc_metrics_fill_na_value |
Fill any ‘NA’ values found in the columns specified with –var_qc_metrics to ‘True’ or ‘False’. as False. | boolean |
--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 , 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" |
Metrics added to .var
Name | Description | Attributes |
---|---|---|
--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 --num_nonzero_obs but percentage based. |
string , default: "pct_dropout" |
Outputs
Name | Description | Attributes |
---|---|---|
--output |
Output h5mu file. | file , example: "output.h5mu" |
--output_compression |
The compression format to be used on the output h5mu object. | string , example: "gzip" |