Concatenate h5mu

Concatenates several uni-modal samples in .h5mu files into a single file

Info

ID: concatenate_h5mu
Namespace: dataflow

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/dataflow/concatenate_h5mu/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: ["sample_paths"]
# input_id: ["foo"]
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
obs_sample_name: "sample_id"
other_axis_mode: "move"

# 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/dataflow/concatenate_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 Paths to the different samples to be concatenated. List of file, required, example: "sample_paths", multiple_sep: ";"
--input_id Names of the different samples that have to be concatenated. Must be specified when using ‘–mode move’. In this case, the ids will be used for the columns names of the dataframes registring the conflicts. If specified, must be of same length as --input. List of string, multiple_sep: ";"
--output file, example: "output.h5mu"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"
--obs_sample_name Name of the .obs key under which to add the sample names. string, default: "sample_id"
--other_axis_mode How to handle the merging of other axis (var, obs, …). - None: keep no data - same: only keep elements of the matrices which are the same in each of the samples - unique: only keep elements for which there is only 1 possible value (1 value that can occur in multiple samples) - first: keep the annotation from the first sample - only: keep elements that show up in only one of the objects (1 unique element in only 1 sample) - move: identical to ‘same’, but moving the conflicting values to .varm or .obsm string, default: "move"

Authors

  • Dries Schaumont (maintainer)