Filter 10xh5

Filter a 10x h5 dataset

Info

ID: filter_10xh5
Namespace: process_10xh5

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/process_10xh5/filter_10xh5/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: "pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"
# output: "$id.$key.output.h5"
min_library_size: 0
min_cells_per_gene: 0
# keep_feature_types: ["Antibody Capture"]
verbose: false

# 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/process_10xh5/filter_10xh5/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 An h5 file from the 10x genomics website. file, required, example: "pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"
--output Output h5 file. file, required, example: "pbmc_1k_protein_v3_raw_feature_bc_matrix_filtered.h5"
--min_library_size Minimum library size. integer, default: 0
--min_cells_per_gene Minimum number of cells per gene. integer, default: 0
--keep_feature_types Specify which feature types will never be filtered out List of string, example: "Antibody Capture", multiple_sep: ";"
--verbose Increase verbosity boolean_true

Authors

  • Robrecht Cannoodt (maintainer)