Grep annotation column

Perform a regex lookup on a column from the annotation matrices .obs or .var.

Info

ID: grep_annotation_column
Namespace: metadata

The annotation matrix can originate from either a modality, or all modalities (global .var or .obs)

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/metadata/grep_annotation_column/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
input: # please fill in - example: "sample_path"
# input_column: "foo"
# input_layer: "foo"
modality: # please fill in - example: "rna"
# matrix: "var"

# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
output_match_column: # please fill in - example: "foo"
# output_fraction_column: "foo"

# Query options
regex_pattern: # please fill in - example: "^[mM][tT]-"

# 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/metadata/grep_annotation_column/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Arguments related to the input dataset.

Name Description Attributes
--input Path to the input .h5mu. file, required, example: "sample_path"
--input_column Column to query. If not specified, use .var_names or .obs_names, depending on the value of –matrix string
--input_layer Input data to use when calculating fraction of observations that match with the query. Only used when –output_fraction_column is provided. If not specified, .X is used. string
--modality Which modality to get the annotation matrix from. string, required, example: "rna"
--matrix Matrix to fetch the column from that will be searched. string, example: "var"

Outputs

Arguments related to how the output will be written.

Name Description Attributes
--output file, example: "output.h5mu"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"
--output_match_column Name of the column to write the result to. string, required
--output_fraction_column For the opposite axis, name of the column to write the fraction of observations that matches to the pattern. string

Query options

Options related to the query

Name Description Attributes
--regex_pattern Regex to use to match with the input column. string, required, example: "^[mM][tT]-"

Authors

  • Dries Schaumont (maintainer)