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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
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Test full profile is not working #123

Open nschcolnicov opened 9 months ago

nschcolnicov commented 9 months ago

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 commented 9 months ago

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

maxulysse commented 9 months ago

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)"