Delimit fraction

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


ID: delimit_fraction
Namespace: filter

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 0.12.6 -latest \
  -main-script target/nextflow/filter/delimit_fraction/ \

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 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/filter/delimit_fraction/ \
  -params-file params.yaml

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups


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"


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


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


  • Dries Schaumont (author, maintainer)