Hi, does anybody know what is the problem with passing

--vep_custom_args

?

nextflow run nf-core/sarek -r 4bd2948 \

-w /str/temp \

-c custom.config \

-C my_nextflow.config \

--input varcall_new.csv \

--outdir Results \

--genome GATK.GRCh38 \

--step variant_calling \

--only_paired_variant_calling \

--normalize_vcfs true \

--tools freebayes,vep \

--vep_custom_args "--merged --offline --mane --force_overwrite --vcf --everything --af_gnomade --af_gnomadg --clinvar_somatic_classification" \

-resume

I'm getting this error: ERROR ~ Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details The following invalid input values have been detected: * --vep_custom_args (true): Value is [boolean] but should be [string] Thanks

Which Sarek and Nextflow version?

are you using nextflow 26.04.0? (check via

nextflow info

)

nextflow 25.10.2 and sarek 3.8.1 (

-r 4bd2948

)

The command line you posted looks good to me, but just make sure that in your actual script the argument string is not somehow disconnected (e.g. on a new line) from the

--vep_custom_args

, because that's what the error message indicates.