Prepared STARIndex folder is missing for GATK/GRCh38

[bounlu]

Description of the bug

I am using the GATK bundle with the below reference genome annotations. However, STARIndex folder is missing in GATK/GRCh38 folder so the pipeline uses the one from NCBI/GRCh38 for the alignment options by default. This causes compatibility issues.

nextflow run nf-core/rnavar \
-latest \
-profile docker \
--genome GRCh38 \
--read_length 150 \
--fasta 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta' \
--dbsnp 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz' \
--dbsnp_tbi 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi' \
--known_indels 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz' \
--known_indels_tbi 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi' \
--annotate_tools merge \
--snpeff_db 'GRCh38.99' \
--vep_species 'homo_sapiens' \
--vep_genome 'GRCh38' \
--vep_cache_version \'107\' \
--input 'samplesheet_rnaseq.csv' \
--outdir 'nextflow/rnavar/results/' \
-work-dir 'nextflow/rnavar/work/' \
-c 'custom.config' \
-r dev \
-resume

Reference genome options
  genome           : GRCh38
  fasta            : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  gtf              : s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf
  read_length      : 150
  known_indels     : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  known_indels_tbi : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
  dbsnp            : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi        : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  snpeff_db        : GRCh38.99
  vep_genome       : GRCh38
  vep_species      : homo_sapiens
  vep_cache_version: '107'

Alignment options
  star_index       : s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/
  star_twopass     : true

Command exit status:
  105

Command output:
  	STAR --genomeDir STARIndex --readFilesIn RLC_AL70_60_1.fq.gz RLC_AL70_60_2.fq.gz --runThreadN 12 --outFileNamePrefix RLC_AL70_60. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:RLC_AL70_60 SM:RLC_AL70_60 PL:illumina --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --sjdbOverhang 149 --twopassMode Basic --outBAMsortingBinsN 50 --limitOutSJcollapsed 1000000
  	STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
  Oct 10 09:19:03 ..... started STAR run
  Oct 10 09:19:03 ..... loading genome

Command error:
  Unable to find image 'quay.io/biocontainers/star:2.7.9a--h9ee0642_0' locally
  2.7.9a--h9ee0642_0: Pulling from biocontainers/star
  c1a16a04cedd: Already exists
  4ca545ee6d5d: Already exists
  f3d7726cfdb6: Pulling fs layer
  f3d7726cfdb6: Verifying Checksum
  f3d7726cfdb6: Download complete
  f3d7726cfdb6: Pull complete
  Digest: sha256:d80ae2e0354e890d55ad0009e9ad9667d1113a679659071e6e02d50e46c8bba1
  Status: Downloaded newer image for quay.io/biocontainers/star:2.7.9a--h9ee0642_0
  
  EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a
  SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a
  
  Oct 10 09:19:03 ...... FATAL ERROR, exiting