qc/calculate_atac_qc_metrics

Description

Add basic ATAC quality control metrics to an .h5mu file.

The metrics are comparable to what scanpy.pp.calculate_qc_metrics output,
although they have slightly different names:

Obs metrics (name in this component -> name in scanpy):

n_features_per_cell -> n_genes_by_counts
total_fragment_counts -> total_counts

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "atac" ]  
n_fragments_for_nucleosome_signal: [ 100000 ]  
nuc_signal_threshold: [ 2 ]  
n_tss: [ 3000 ]  
tss_threshold: [ 1.5 ]  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.3 \  
  -main-script target/nextflow/qc/calculate_atac_qc_metrics/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file
--fragments_path	file	Path to the fragments file. If not provided and not present in the input h5mu file, the nucleosome signal and TSS enrichment score will not be calculated.
--modality	string	Which modality from the input MuData file to process.
--layer	string	Layer at `.layers` to use for the calculation. If not provided, `.X` is used.
--n_fragments_for_nucleosome_signal	integer	Number of fragments to use per cell for nucleosome signal calculation. Takes very long to calculate, for a test run lower value (e.g. 10e3) is recommended. See https://www.sc-best-practices.org/chromatin_accessibility/quality_control.html#nucleosome-signal for more information
--nuc_signal_threshold	double	Threshold for nucleosome signal. Cells with nucleosome signal above this threshold will be marked as low quality ("NS_FAIL"), otherwise they will be marked "NS_PASS".
--n_tss	integer	Number of the transcription start sites to calculate TSS enrichment score. See https://www.sc-best-practices.org/chromatin_accessibility/quality_control.html#tss-enrichment for more information
--tss_threshold	double	Threshold for TSS enrichment score. Cells with TSS enrichment score below this threshold will be marked as low quality ("TSS_FAIL") otherwise they will be marked as "TSS_PASS".

Name

Type & Properties

--input

file

required

--fragments_path

file

--modality

string

--layer

string

--n_fragments_for_nucleosome_signal

integer

--nuc_signal_threshold

double

--n_tss

integer

--tss_threshold

double

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

output

--output_compression

string