Test full profile is not working

[nschcolnicov]

Description of the bug

When trying to run the test_full profile I get the error: Known variants VCF file or its index is missing!. At least --dbsnp (and its index) or --known_indels (and its index) is required.

Command used and terminal output

Both of these commands raise the same error
nextflow run ../../main.nf -profile test_full,bi,cluster --outdir .

nextflow run ../main.nf -profile test_full,docker --outdir .

Relevant files

No response

System information

dev branch

[maxulysse]

Fully agreeing on that, need to refactor the whole references genome handling

[maxulysse]

any chance adding that make this work:

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,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz](s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/%7BMills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels%7D.vcf.gz)"
known_indels_tbi: "[s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi](s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/%7BMills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels%7D.vcf.gz.tbi)"