Htseq count to h5mu

Convert the htseq table to a h5mu


ID: htseq_count_to_h5mu
Namespace: mapping

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/mapping/htseq_count_to_h5mu/ \

Run command

Example of params.yaml
# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"

# Input
input_id: # please fill in - example: ["foo"]
input_counts: # please fill in - example: ["counts.tsv"]
reference: # please fill in - example: "gencode_v41_star"

# 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/mapping/htseq_count_to_h5mu/ \
  -params-file params.yaml

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

Argument groups


Name Description Attributes
--input_id The obs index for the counts List of string, required, example: "foo", multiple_sep: ";"
--input_counts The counts as a TSV file as output by HTSeq. List of file, required, example: "counts.tsv", multiple_sep: ";"
--reference The GTF file. file, required, example: "gencode_v41_star"


Name Description Attributes
--output Output h5mu file. file, required, example: "output.h5mu"
--output_compression The compression format to be used on the output h5mu object. string, example: "gzip"


  • Robrecht Cannoodt (author, maintainer)

  • Angela Oliveira Pisco (author)