Do filter

Remove observations and variables based on specified .obs and .var columns

Info

ID: do_filter
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/do_filter/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "input.h5mu"
modality: "rna"
# obs_filter: ["filter_with_x"]
# var_filter: ["filter_with_x"]
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"

# 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/do_filter/main.nf \
  -params-file params.yaml

Note

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

Argument group

Arguments

Name	Description	Attributes
--input	Input h5mu file	file, required, example: "input.h5mu"
--modality		string, default: "rna"
--obs_filter	Which .obs columns to use to filter the observations by.	List of string, example: "filter_with_x", multiple_sep: ";"
--var_filter	Which .var columns to use to filter the observations by.	List of string, example: "filter_with_x", multiple_sep: ";"
--output	Output h5mu file.	file, example: "output.h5mu"
--output_compression	The compression format to be used on the output h5mu object.	string, example: "gzip"

Authors

• Robrecht Cannoodt (maintainer, contributor)