From bdrhap to h5mu

Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file

Info

ID: from_bdrhap_to_h5mu
Namespace: convert

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 2.1.1 -latest \
  -main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
id: # please fill in - example: "my_id"
input: # please fill in - example: "sample.h5mu"

# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

# Arguments

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/convert/from_bdrhap_to_h5mu/main.nf \
  -params-file params.yaml

Note

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

Argument groups

Inputs

Name	Description	Attributes
--id	A sample ID.	string, required, example: "my_id"
--input	The output h5mu of a BD Rhapsody workflow.	file, required, example: "sample.h5mu"

Outputs

Name	Description	Attributes
--output	Output h5mu file.	file, required, example: "output.h5mu"
--output_compression		string, example: "gzip"

Authors

• Dorien Roosen (author, maintainer)

• Robrecht Cannoodt (author)