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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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GenomicsDBImport fails when no_intervals is set to true #1434

Open saulpierotti opened 8 months ago

saulpierotti commented 8 months ago

Description of the bug

This is likely due to the GenomicsDBImport module calling the tool with the flag --intervals [] (with a literal []). Attached the log.

Command used and terminal output

nextflow run nf-core/sarek \
        -c nextflow.config \
        -params-file params.yaml \
        -r 3.4.0 \
        -profile singularity,slurm

Relevant files

sarek_logs_and_inputs.tar.gz

System information

No response

FriederikeHanssen commented 8 months ago

Hmmm so this is somewhat expected because the tool needs intervals, however this should be caught by the input validation. Thanks for reporting

cmatKhan commented 3 months ago

When --no_intervals is true, the GATK workflow could use combineGVCFs instead

https://gatk.broadinstitute.org/hc/en-us/articles/360037053272-CombineGVCFs