reference/build_star_reference
Description
Create a reference for STAR from a set of fasta files.
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. |
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). |
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 v4.2.0 \
-main-script target/nextflow/reference/build_star_reference/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
reference/build_star_referenceopenpipeline v4.2.0
Uses
0 relationships
No component dependencies found.