11.1. STAR Genomic Indexes

The genome.fa and genes.gtf files should be copied to the genome directory.

localhost:~> mkdir genome
localhost:~> cd genome
localhost:~> mkdir STAR
localhost:~> cd STAR
localhost:~> cwl-runner https://github.com/ncbi/cwl-ngs-workflows-cbb/blob/master/tools/star/star-index.cwl --runThreadN 16 --genomeDir . --genomeFastaFiles ../genome.fa  --sjdbGTFfile ../genes.gtf
localhost:~> cd ..
localhost:~> tree
.
├── genes.gtf
├── genome.fa
└── STAR
    ├── chrLength.txt
    ├── chrNameLength.txt
    ├── chrName.txt
    ├── chrStart.txt
    ├── exonGeTrInfo.tab
    ├── exonInfo.tab
    ├── geneInfo.tab
    ├── Genome
    ├── genomeParameters.txt
    ├── Log.out
    ├── SA
    ├── SAindex
    ├── sjdbInfo.txt
    ├── sjdbList.fromGTF.out.tab
    ├── sjdbList.out.tab
    └── transcriptInfo.tab

1 directory, 18 files

Here all files inside the directory STAR are created by the workflow.