reference/build_bdrhap_reference

Description

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

STAR index
Filtered GTF file

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
reference_archive: "$id.$key.reference_archive.gz"  
mitochondrial_contigs: [ "chrM", "chrMT", "M", "MT" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/reference/build_bdrhap_reference/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--genome_fasta	file required multiple	Reference genome file in FASTA or FASTA.GZ format. The BD Rhapsody Sequencing Analysis Pipeline uses GRCh38 for Human and GRCm39 for Mouse.
--gtf	file required multiple	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.
--extra_sequences	file multiple	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.

Name

Type & Properties

--genome_fasta

file

required

multiple

--gtf

file

required

multiple

--extra_sequences

file

multiple

Outputs

Name	Type & Properties	Description
--reference_archive	file required output	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.

Name

Type & Properties

--reference_archive

file

required

output

Arguments

Name	Type & Properties	Description
--mitochondrial_contigs	string multiple	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.
--filtering_off	boolean_true	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.
--wta_only_index	boolean_true	Build a WTA only index, otherwise builds a WTA + ATAC index.
--extra_star_params	string	Additional parameters to pass to STAR when building the genome index. Specify exactly like how you would on the command line.

Name

Type & Properties

--mitochondrial_contigs

string

multiple

--filtering_off

boolean_true

--wta_only_index

boolean_true

--extra_star_params

string