how to use custom vep database for microbe, such as Candian.aruis

[ybdong919]

Description of the bug

custom vep annotation seems not working for microbe, such as Candian.aruis, sars_cov2, etc.

Command used and terminal output

N E X T F L O W ~ version 24.04.4

Launching ./sarek/main.nf [nostalgic_wescoff] DSL2 - revision: 1eeed174dc

WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value

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nf-core/sarek v3.5.0dev

Core Nextflow options
runName : nostalgic_wescoff
containerEngine : singularity
launchDir : /blue/bphl-florida/dongyibo/nf-core/sarek3
workDir : /blue/bphl-florida/dongyibo/nf-core/sarek3/work
projectDir : /blue/bphl-florida/dongyibo/nf-core/sarek3/sarek
userName : dongyibo
profile : singularity
configFiles :

Input/output options
input : ./samplesheet.csv
outdir : ./results/

Main options
tools : freebayes,strelka,snpeff,vep
skip_tools : baserecalibrator,baserecalibrator_report,dnascope_filter

Variant Calling
only_paired_variant_calling: true

Reference genome options
fasta : /blue/bphl-florida/dongyibo/nf-core/sarek3/data/reference/covid/nCoV-2019.reference.fasta
fasta_fai : /blue/bphl-florida/dongyibo/nf-core/sarek3/data/reference/covid/nCoV-2019.reference.fasta.fai
snpeff_db : MN908947.3
vep_genome : MN908947.3
vep_species : sars_cov2
igenomes_ignore : true
vep_cache : /blue/bphl-florida/dongyibo/nf-core/sarek3/data/vep_cache
snpeff_cache : /blue/bphl-florida/dongyibo/nf-core/sarek3/data/snpeff_cache

Generic options
validationLenientMode : true

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/sarek for your analysis please cite:

• The pipeline
  https://doi.org/10.12688/f1000research.16665.2
  https://doi.org/10.1093/nargab/lqae031
  https://doi.org/10.5281/zenodo.3476425

• The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

• Software dependencies
  https://github.com/nf-core/sarek/blob/master/CITATIONS.md

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[- ] NFC…EPARE_GENOME:BWAMEM1_INDEX -
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[- ] NFC…4_CREATESEQUENCEDICTIONARY -

[- ] NFC…EPARE_GENOME:BWAMEM1_INDEX -
[- ] NFC…EPARE_GENOME:BWAMEM2_INDEX -
[- ] NFC…E_GENOME:DRAGMAP_HASHTABLE -
[- ] NFC…4_CREATESEQUENCEDICTIONARY -
[- ] NFC…E_GENOME:MSISENSORPRO_SCAN -
[- ] NFC…PARE_GENOME:SAMTOOLS_FAIDX -
[- ] NFC…TABIX_BCFTOOLS_ANNOTATIONS -
[- ] NFC…PREPARE_GENOME:TABIX_DBSNP -
[- ] NFC…ME:TABIX_GERMLINE_RESOURCE -
[- ] NFC…RE_GENOME:TABIX_KNOWN_SNPS -
[- ] NFC…_GENOME:TABIX_KNOWN_INDELS -
[- ] NFC…K:PREPARE_GENOME:TABIX_PON -
[- ] NFC…_INTERVALS:BUILD_INTERVALS -
[- ] NFC…RVALS:CREATE_INTERVALS_BED -
Path provided with VEP cache is invalid.
Make sure there is a directory named sars_cov2/null_MN908947.3 in /blue/bphl-florida/dongyibo/nf-core/sarek3/data/vep_cache./nPlease refer to https://nf-co.re/sarek/docs/usage/#how-to-customise-snpeff-and-vep-annotation for more information.

Relevant files

No response

System information

No response