Delimit fraction

Turns a column containing values between 0 and 1 into a boolean column based on thresholds

Info

ID: delimit_fraction
Namespace: filter

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 1.0.1 -latest \
  -main-script target/nextflow/filter/delimit_fraction/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
input: # please fill in - example: "input.h5mu"
modality: "rna"
# layer: "raw_counts"
obs_fraction_column: # please fill in - example: "fraction_mitochondrial"

# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
obs_name_filter: # please fill in - example: "foo"

# Arguments
min_fraction: 0
max_fraction: 1

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

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/filter/delimit_fraction/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
--input	Input h5mu file	file, required, example: "input.h5mu"
--modality		string, default: "rna"
--layer		string, example: "raw_counts"
--obs_fraction_column	Name of column from .var dataframe selecting a column that contains floating point values between 0 and 1.	string, required, example: "fraction_mitochondrial"

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"
--obs_name_filter	In which .obs slot to store a boolean array corresponding to which observations should be removed.	string, required

Arguments

Name	Description	Attributes
--min_fraction	Min fraction for an observation to be retained (True in output).	double, default: 0
--max_fraction	Max fraction for an observation to be retained (True in output).	double, default: 1

Authors

• Dries Schaumont (author, maintainer)