Closed
Description
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:
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_resultsRelevant 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