From 10xmtx to h5mu

Converts a 10x mtx into an h5mu file

Info

ID: from_10xmtx_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 1.0.2 -latest \
  -main-script target/nextflow/convert/from_10xmtx_to_h5mu/main.nf \
  --help

Run command

Example of params.yaml

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

# 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_10xmtx_to_h5mu/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 mtx folder	file, required, example: "input_dir_containing_gz_files"
--output	Output h5mu file.	file, example: "output.h5mu"
--output_compression		string, example: "gzip"

Authors

• Robrecht Cannoodt (maintainer)