From 10xh5 to h5mu

Converts a 10x h5 into an h5mu file

Info

ID: from_10xh5_to_h5mu
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 0.12.6 -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 0.12.6 -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)