Build bdrhap reference

Compile a reference into a STAR index compatible with the BD Rhapsody pipeline.

Info

ID: build_bdrhap_reference
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 1.0.1 -latest \
  -main-script target/nextflow/reference/build_bdrhap_reference/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
genome_fasta: # please fill in - example: "genome_sequence.fa.gz"
transcriptome_gtf: # please fill in - example: "transcriptome_annotation.gtf.gz"
# output: "$id.$key.output.gz"

# 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/reference/build_bdrhap_reference/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
--genome_fasta	Reference genome fasta.	file, required, example: "genome_sequence.fa.gz"
--transcriptome_gtf	Reference transcriptome annotation.	file, required, example: "transcriptome_annotation.gtf.gz"
--output	Star index	file, required, example: "star_index.tar.gz"

Authors

• Angela Oliveira Pisco (author)

• Robrecht Cannoodt (author, maintainer)