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
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. |
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. |
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. |
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 v4.2.0 \
-main-script target/nextflow/reference/build_bdrhap_reference/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
reference/build_bdrhap_referenceopenpipeline v4.2.0
Uses
0 relationships
No component dependencies found.