single sample haplotypecaller with no dbsnp causes error because of missing dbsnp_tbi

[cmatKhan]

Description of the bug

Using haplotypecaller without passing a --dbsnp, the following error is raised:

ERROR ~ Cannot get property 'baseName' on null object

 -- Check script '/scratch/mblab/chasem/nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/main.nf' at line: 132 or see '.nextflow.log' file for more details
ERROR ~ Cannot get property 'baseName' on null object

 -- Check script '/scratch/mblab/chasem/nextflow/assets/nf-core/sarek/./workflows/sarek/../../subworkflows/local/bam_variant_calling_germline_all/main.nf' at line: 133 or see '.nextflow.log' file for more details
-[nf-core/sarek] Pipeline completed with errors-

If I replace this line:

sarek/subworkflows/local/bam_variant_calling_germline_all/main.nf

Line 133 in b5b766d

dbsnp_tbi.map{ it -> [[id:it[0].baseName], it] },

with

[[:], []]

the subworkflow completes without error.

Sorry for the lack of a reproducible example for the time being -- will try to make one early next week.

Command used and terminal output

nextflow run nf-core/sarek -profile singularity -params-file bam_input_params.json -c /scratch/mblab/chasem/bsa/wustl_htcf.config -c kn99.config --input samplesheets/run_6991.csv --outdir run_6991_results

Relevant files

I tried this with haplotypecaller_filter in "skip_tools", also, with the same result.

{
    "tools": "haplotypecaller,manta,cnvkit,snpeff",
    "skip_tools": "baserecalibrator",
    "joint_germline": false,
    "genome": "",
    "dbsnp_vqsr": false,
    "fasta": "\/ref\/mblab\/data\/KN99\/KN99_genome_fungidb.fasta",
    "fasta_fai": "\/ref\/mblab\/data\/KN99\/KN99_genome_fungidb.fasta.fai",
    "known_indels_vqsr": false,
    "known_snps": false,
    "known_snps_tbi": false,
    "known_snps_vqsr": false,
    "ngscheckmate_bed": false,
    "snpeff_db": "1",
    "snpeff_genome": "ASM221672v1",
    "igenomes_ignore": true,
    "vep_cache": "",
    "snpeff_cache": "\/ref\/mblab\/data\/KN99\/snpeff_db",
    "split_fastq": 1000000,
    "nucleotides_per_second": 10000,
    "save_output_as_bam": true,
    "step": "prepare_recalibration"
}

System information

Nextflow: 24.04.2
Hardware: HPC
Executor: SLURM
Container engine: Singularityce
OS: Rocky linux v8.9
nf-core/sarek: 3.4.2

[FriederikeHanssen]

Thanks for finding this. Added it to the 3.5 milestones

[drowsygoat]

I can confirm the same problem while using a "non-standard" genome with no known reference variants. Is there any known workaround?

nf-core/sarek v3.4.3-ge92242e
engine: singularity
nf version 24.04.4

[cmatKhan]

you have to edit the code on your local version for the moment until it gets corrected and released, but the correction i described in the original post works. Depending on what options you have set, there are a couple other spots that the same correction needs to be made.