star/star_genome_generate

genome

index

align

Description

Create index for STAR

Type

bash_script

License

MIT

Keywords

genome

index

align

Links

Repository

Documentation

Launch

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 v0.1.0 \  
  -main-script target/nextflow/star/star_genome_generate/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--genomeFastaFiles	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.
--sjdbGTFfile	file	Path to the GTF file with annotations
--sjdbOverhang	integer	Length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)
--sjdbGTFchrPrefix	string	Prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC genomes)
--sjdbGTFfeatureExon	string	Feature type in GTF file to be used as exons for building transcripts
--sjdbGTFtagExonParentTranscript	string	GTF attribute name for parent transcript ID (default "transcript_id" works for GTF files)
--sjdbGTFtagExonParentGene	string	GTF attribute name for parent gene ID (default "gene_id" works for GTF files)
--sjdbGTFtagExonParentGeneName	string multiple	GTF attribute name for parent gene name
--sjdbGTFtagExonParentGeneType	string multiple	GTF attribute name for parent gene type
--limitGenomeGenerateRAM	long	Maximum available RAM (bytes) for genome generation
--genomeSAindexNbases	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).
--genomeChrBinNbits	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)]).
--genomeSAsparseD	integer	Suffux array sparsity, i.e. distance between indices. Use bigger numbers to decrease needed RAM at the cost of mapping speed reduction.
--genomeSuffixLengthMax	integer	Maximum length of the suffixes, has to be longer than read length. Use -1 for infinite length.
--genomeTransformType	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)
--genomeTransformVCF	file	path to VCF file for genome transformation

Name

Type & Properties

--genomeFastaFiles

file

required

multiple

--sjdbGTFfile

file

--sjdbOverhang

integer

--sjdbGTFchrPrefix

string

--sjdbGTFfeatureExon

string

--sjdbGTFtagExonParentTranscript

string

--sjdbGTFtagExonParentGene

string

--sjdbGTFtagExonParentGeneName

string

multiple

--sjdbGTFtagExonParentGeneType

string

multiple

--limitGenomeGenerateRAM

long

--genomeSAindexNbases

integer

--genomeChrBinNbits

integer

--genomeSAsparseD

integer

--genomeSuffixLengthMax

integer

--genomeTransformType

string

--genomeTransformVCF

file

Output

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

Name

Type & Properties

--index

file

required

output