From h5mu to seurat

Converts an h5mu file into a Seurat file.

Info

ID: from_h5mu_to_seurat
Namespace: convert

Links

Restrictions: - Only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation. - Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay. - Embeddings names are changed in order to comply with R & Seurat requirements and conventions. - Feature names with underscores (’_‘) are automatically replaced with dashes (’-’) - Seurat does not support global variables metadata /var.

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/convert/from_h5mu_to_seurat/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input: # please fill in - example: "input.h5mu"
# output: "$id.$key.output.rds"

# 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/convert/from_h5mu_to_seurat/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"`
`--output`	Output Seurat file	`file`, required, example: `"output.rds"`

Authors

Robrecht Cannoodt (author, maintainer)