From 10xh5 to h5mu

Converts a 10x h5 into an h5mu file

Info

ID: from_10xh5_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 1.0.1 -latest \
  -main-script target/nextflow/convert/from_10xh5_to_h5mu/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
input: # please fill in - example: "raw_feature_bc_matrix.h5"
# input_metrics_summary: "metrics_cellranger.h5"

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

# Arguments
# min_genes: 100
# min_counts: 1000

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

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/convert/from_10xh5_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	A 10x h5 file as generated by Cell Ranger.	file, required, example: "raw_feature_bc_matrix.h5"
--input_metrics_summary	A metrics summary csv file as generated by Cell Ranger.	file, example: "metrics_cellranger.h5"

Outputs

Name	Description	Attributes
--output	Output h5mu file.	file, example: "output.h5mu"
--output_compression		string, example: "gzip"
--uns_metrics	Name of the .uns slot under which to QC metrics (if any).	string, default: "metrics_cellranger"

Arguments

Name	Description	Attributes
--min_genes	Minimum number of counts required for a cell to pass filtering.	integer, example: 100
--min_counts	Minimum number of genes expressed required for a cell to pass filtering.	integer, example: 1000

Authors

• Robrecht Cannoodt (maintainer)