Build bdrhap reference

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

Info

ID: build_bdrhap_reference
Namespace: reference

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/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 0.12.6 -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)