star/star_genome_generate

genome

index

align

Description

Create index for STAR

Input

Name	Type & Properties	Description
--genome_fasta_files	file required multiple	Path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they cannot be zipped.
--sjdb_gtf_file	file	Path to the GTF file with annotations
--sjdb_overhang	integer	Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)
--sjdb_gtf_chr_prefix	string	Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC genomes)
--sjdb_gtf_feature_exon	string	Feature type in GTF file to be used as exons for building transcripts
--sjdb_gtf_tag_exon_parent_transcript	string	GTF attribute name for parent transcript ID (default "transcript_id" works for GTF files)
--sjdb_gtf_tag_exon_parent_gene	string	GTF attribute name for parent gene ID (default "gene_id" works for GTF files)
--sjdb_gtf_tag_exon_parent_gene_name	string multiple	GTF attribute name for parent gene name
--sjdb_gtf_tag_exon_parent_gene_type	string multiple	GTF attribute name for parent gene type
--limit_genome_generate_ram	long	Maximum available RAM (bytes) for genome generation
--genome_sa_index_nbases	integer	Length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, this parameter must be scaled down to min(14, log2(GenomeLength)/2 - 1).
--genome_chr_bin_nbits	integer	Defined as log2(chrBin), where chrBin is the size of the bins for genome storage. Each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]).
--genome_sa_sparse_d	integer	Suffux array sparsity, i.e. distance between indices. Use bigger numbers to decrease needed RAM at the cost of mapping speed reduction.
--genome_suffix_length_max	integer	Maximum length of the suffixes, has to be longer than read length. Use -1 for infinite length.
--genome_transform_type	string	Type of genome transformation None ... no transformation Haploid ... replace reference alleles with alternative alleles from VCF file (e.g. consensus allele) Diploid ... create two haplotypes for each chromosome listed in VCF file, for genotypes 1\|2, assumes perfect phasing (e.g. personal genome)
--genome_transform_vcf	file	path to VCF file for genome transformation

Name

Type & Properties

--genome_fasta_files

file

required

multiple

--sjdb_gtf_file

file

--sjdb_overhang

integer

--sjdb_gtf_chr_prefix

string

--sjdb_gtf_feature_exon

string

--sjdb_gtf_tag_exon_parent_transcript

string

--sjdb_gtf_tag_exon_parent_gene

string

--sjdb_gtf_tag_exon_parent_gene_name

string

multiple

--sjdb_gtf_tag_exon_parent_gene_type

string

multiple

--limit_genome_generate_ram

long

--genome_sa_index_nbases

integer

--genome_chr_bin_nbits

integer

--genome_sa_sparse_d

integer

--genome_suffix_length_max

integer

--genome_transform_type

string

--genome_transform_vcf

file

Output

Name	Type & Properties	Description
--index	file required output	STAR index directory.

Name

Type & Properties

--index

file

required

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
index: "$id.$key.index"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.2 \  
  -main-script target/nextflow/star/star_genome_generate/main.nf \  
  -params-file params.yaml

star/star_genome_generate

Input

Output

Run this component

Relationships

Used by

Uses