Build bdrhap reference

The Reference Files Generator creates an archive containing Genome Index and Transcriptome annotation files needed for the BD Rhapsody Sequencing Analysis Pipeline.

Info

ID: build_bdrhap_reference
Namespace: reference

The app takes as input one or more FASTA and GTF files and produces a compressed archive in the form of a tar.gz file. The archive contains:

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/build_bdrhap_reference/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
genome_fasta: # please fill in - example: ["genome_sequence.fa.gz"]
gtf: # please fill in - example: ["transcriptome_annotation.gtf.gz"]
# extra_sequences: ["path/to/file"]

# Outputs
# reference_archive: "$id.$key.reference_archive.gz"

# Arguments
mitochondrial_contigs: ["chrM", "chrMT", "M", "MT"]
filtering_off: false
wta_only_index: false
# extra_star_params: "--limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11"

# 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/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 groups

Inputs

Name Description Attributes
--genome_fasta Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse. List of file, required, example: "genome_sequence.fa.gz", multiple_sep: ";"
--gtf File path to the transcript annotation files in GTF or GTF.GZ format. The Sequence Analysis Pipeline requires the ‘gene_name’ or ‘gene_id’ attribute to be set on each gene and exon feature. Gene and exon feature lines must have the same attribute, and exons must have a corresponding gene with the same value. For TCR/BCR assays, the TCR or BCR gene segments must have the ‘gene_type’ or ‘gene_biotype’ attribute set, and the value should begin with ‘TR’ or ‘IG’, respectively. List of file, required, example: "transcriptome_annotation.gtf.gz", multiple_sep: ";"
--extra_sequences File path to additional sequences in FASTA format to use when building the STAR index. (e.g. transgenes or CRISPR guide barcodes). GTF lines for these sequences will be automatically generated and combined with the main GTF. List of file, multiple_sep: ";"

Outputs

Name Description Attributes
--reference_archive A Compressed archive containing the Reference Genome Index and annotation GTF files. This archive is meant to be used as an input in the BD Rhapsody Sequencing Analysis Pipeline. file, required, example: "reference.tar.gz"

Arguments

Name Description Attributes
--mitochondrial_contigs Names of the Mitochondrial contigs in the provided Reference Genome. Fragments originating from contigs other than these are identified as ‘nuclear fragments’ in the ATACseq analysis pipeline. List of string, default: "chrM", "chrMT", "M", "MT", multiple_sep: ";"
--filtering_off By default the input Transcript Annotation files are filtered based on the gene_type/gene_biotype attribute. Only features having the following attribute values are kept: - protein_coding - lncRNA - IG_LV_gene - IG_V_gene - IG_V_pseudogene - IG_D_gene - IG_J_gene - IG_J_pseudogene - IG_C_gene - IG_C_pseudogene - TR_V_gene - TR_V_pseudogene - TR_D_gene - TR_J_gene - TR_J_pseudogene - TR_C_gene If you have already pre-filtered the input Annotation files and/or wish to turn-off the filtering, please set this option to True. boolean_true
--wta_only_index Build a WTA only index, otherwise builds a WTA + ATAC index. boolean_true
--extra_star_params Additional parameters to pass to STAR when building the genome index. Specify exactly like how you would on the command line. string, example: "--limitGenomeGenerateRAM 48000 --genomeSAindexNbases 11"

Authors

  • Robrecht Cannoodt (author, maintainer)

  • Weiwei Schultz (contributor)