Velocyto to h5mu

Convert a velocyto loom file to a h5mu file.

Info

ID: velocyto_to_h5mu
Namespace: convert

If an input h5mu file is also provided, the velocity h5ad object will get added to that h5mu instead.

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/velocyto_to_h5mu/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
input_loom: # please fill in - example: "input.loom"
# input_h5mu: "input.h5mu"
modality: "rna_velocity"

# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
layer_spliced: "velo_spliced"
layer_unspliced: "velo_unspliced"
layer_ambiguous: "velo_ambiguous"

# 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/velocyto_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
--input_loom Path to the input loom file. file, required, example: "input.loom"
--input_h5mu If a MuData file is provided, file, example: "input.h5mu"
--modality The name of the modality to operate on. string, default: "rna_velocity"

Outputs

Name Description Attributes
--output Path to the output MuData file. file, example: "output.h5mu"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"
--layer_spliced Output layer for the spliced reads. string, default: "velo_spliced"
--layer_unspliced Output layer for the unspliced reads. string, default: "velo_unspliced"
--layer_ambiguous Output layer for the ambiguous reads. string, default: "velo_ambiguous"

Authors

  • Dries Schaumont (maintainer, author)

  • Robrecht Cannoodt (author)

  • Angela Oliveira Pisco (contributor)