Do filter

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

Info

ID: do_filter
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/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 0.12.6 -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)