From h5ad to seurat

Converts an h5ad file into a Seurat file

Info

ID: from_h5ad_to_seurat
Namespace: convert

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 2.1.0 -latest \
  -main-script target/nextflow/convert/from_h5ad_to_seurat/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: "input.h5ad"
assay: "RNA"
# 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 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/convert/from_h5ad_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 h5ad file file, required, example: "input.h5ad"
--assay Name of the assay to be created. string, default: "RNA"
--output Output Seurat file file, required, example: "output.rds"

Authors

  • Robrecht Cannoodt (author, maintainer)