reference/build_star_reference

Description

Create a reference for STAR from a set of fasta files.

Type

python_script

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output./path/to/foo"  
genomeSAindexNbases: [ 14 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 2.0.0 \  
  -main-script target/nextflow/reference/build_star_reference/main.nf \  
  -params-file params.yaml

Input/Output

Name	Type & Properties	Description
--genome_fasta --genomeFastaFiles	file required multiple	The fasta files to be included in the reference. Corresponds to the --genomeFastaFiles argument in the STAR command.
--transcriptome_gtf --sjdbGTFfile	file	Specifies the path to the file with annotated transcripts in the standard GTF format. STAR will extract splice junctions from this file and use them to greatly improve accuracy of the mapping. Corresponds to the --sjdbGTFfile argument in the STAR command.
--output --genomeDir	file required output	Path to output directory. Corresponds to the --genomeDir argument in the STAR command.

Name

Type & Properties

--genome_fasta

--genomeFastaFiles

file

required

multiple

--transcriptome_gtf

--sjdbGTFfile

file

--output

--genomeDir

file

required

output

Genome indexing arguments

Name	Type & Properties	Description
--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, the parameter {genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1).

Name

Type & Properties

--genomeSAindexNbases

integer