mapping/htseq_count_to_h5mu

Description

Convert the htseq table to a h5mu.

Type

python_script

Contributors

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.h5mu"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.3 \  
  -main-script target/nextflow/mapping/htseq_count_to_h5mu/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--input_id	string required multiple	The obs index for the counts
--input_counts	file required multiple	The counts as a TSV file as output by HTSeq.
--reference	file required	The GTF file.

Name

Type & Properties

--input_id

string

required

multiple

--input_counts

file

required

multiple

--reference

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	Output h5mu file.
--output_compression	string	The compression format to be used on the output h5mu object.

Name

Type & Properties

--output

-o

file

required

output

--output_compression

string