SNPEFF annotation process interrupted when no cache available

[ducminhnguyenle]

Description of the bug

I am using the sarek pipeline latest version (3.3.1) with the utilization of sentieon workflow in order to perform joint variant calling using sentieon_gvcftyper for 20 WES samples. However the annotation process with SNPEFF is not working with the following errors:

-[nf-core/sarek] Pipeline completed with errors-
WARN: Input tuple does not match input set cardinality declared by process `NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF` -- offending value: []
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

I have included the nextflow.log file and also the WES_sentieon_jointcalling_headnode.log run log file.

Command used and terminal output

nextflow run main.nf \
    --input /mnt/rdisk/hieule/sarek_sentieon/input/samplesheet.csv \
    --outdir /mnt/rdisk/hieule/sarek_sentieon/output_3.3.1/ \
    -w /mnt/rdisk/hieule/sarek_sentieon/work_dir/ \
    --igenomes_base /mnt/rdisk/hieule/sarek_sentieon/input/references/ \
    --wes \
    --intervals /mnt/rdisk/hieule/sarek_sentieon/input/hg38_Exome_2.0_Plus_Panel_chr.bed \
    -profile docker \
    --aligner sentieon-bwamem \
    --tools sentieon_dedup,sentieon_haplotyper,merge \
    --joint_germline \
    --sentieon_haplotyper_emit_mode gvcf

Relevant files

WES_sentieon_jointcalling_headnode.log
nextflow.log

System information

• Nextflow version 23.04.2
• Hardware: HPC
• Container engine: Docker
• OS: Linux Ubuntu 22.04
• Version of nf-core/sarek: 3.3.1

[asp8200]

Seems related to the tool-option merge and snpeff

nextflow run main.nf -profile test_cache,singularity --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller,merge --step variant_calling --joint_germline --outdir results

gives

ERROR ~ Error executing process > 'NFCORE_SAREK:sarek:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:SNPEFF_SNPEFF (1)'

Caused by:
  Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

on both master and dev.

@maxulysse is on it.

[maxulysse]

Yes, this issue is not related to either sention nor variant calling, but actually just caused by a missing cache for the annotation tool.
I think we'd rather fail early with a proper error than not running the tool, so I have a PR open to fix this issue: #1248

[ducminhnguyenle]

Thank you for your clear explanation. I will have a look to double check again.