Cellranger mkgtf

Make a GTF file - filter by a specific attribute.

Info

ID: cellranger_mkgtf
Namespace: reference

Links

Source

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 2.1.0 -latest \
  -main-script target/nextflow/reference/cellranger_mkgtf/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
input_gtf: # please fill in - example: "transcriptome_annotation.gtf.gz"
# output_gtf: "$id.$key.output_gtf.gz"
attribute: # please fill in - example: ["gene_type:transcribed_unprocessed_pseudogene", "gene_type:miRNA"]

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/reference/cellranger_mkgtf/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_gtf	Reference GTF annotation.	file, required, example: "transcriptome_annotation.gtf.gz"
--output_gtf	Output GTF file.	file, required, example: "output.gtf.gz"
--attribute	Key-value pair in attributes field to be kept in the GTF file of the format attribute:attribute_value.	List of string, required, example: "gene_type:transcribed_unprocessed_pseudogene", "gene_type:miRNA", multiple_sep: ";"

Authors

• Jakub Majercik (author)