Intersect obs

Create an intersection between two or more modalities.

Info

ID: intersect_obs
Namespace: filter

This component removes any observations which are not present in all modalities.

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 1.0.2 -latest \
  -main-script target/nextflow/filter/intersect_obs/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: "input.h5mu"
modalities: # please fill in - example: ["rna", "prot"]
# 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 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/filter/intersect_obs/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"
--modalities List of string, required, example: "rna", "prot", 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

  • Dries Schaumont (maintainer)

  • Isabelle Bergiers (contributor)