Compress h5mu

Compress a MuData file.

Info

ID: compress_h5mu
Namespace: compression

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/compression/compress_h5mu/main.nf \
  --help

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: "sample_path"
# output: "$id.$key.output.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/compression/compress_h5mu/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 Path to the input .h5mu. file, required, example: "sample_path"
--output location of output file. file, required
--compression Compression type. string, default: "gzip"

Authors

  • Dries Schaumont (maintainer)