Space in manta vcf header causes bcftools norm error

[vmkalbskopf]

Description of the bug

I now realise that this pipeline does not support manta output created by sarek, but I post this here for future releases.

This is a filename parsing / channel naming issue in the pipeline rather than a bcftools problem itself.

The process is generating this output filename:

--output HD827.HD827-manta.generatesvcandidates 1.6.0.norm.vcf.gz

Notice the space:

HD827.HD827-manta.generatesvcandidates 1.6.0.norm.vcf.gz
                                      ^

Because of that, bcftools interprets:

HD827.HD827-manta.generatesvcandidates as the output file
1.6.0.norm.vcf.gz as an input argument

So it tries to open:
1.6.0.norm.vcf.gz

Which does not exist, causing:
Failed to open file "1.6.0.norm.vcf.gz"

However, the 1.6.1 comes from the manta vcf header. It is not found in my samplesheet anywhere.

Command used and terminal output

`nextflow run nf-core/variantprioritization -r 1.0.0 -resume -profile singularity -params-file params.yaml`


` Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_VARIANTPRIORITIZATION:VARIANTPRIORITIZATION:INPUT_PREPROCESSING:BCFTOOLS_NORM (HD827.HD827-manta.generatesvcandidates 1.6.0)' Caused by: Process NFCORE_VARIANTPRIORITIZATION:VARIANTPRIORITIZATION:INPUT_PREPROCESSING:BCFTOOLS_NORM (HD827.HD827-manta.generatesvcandidates 1.6.0) terminated with an error exit status (255) Command executed: bcftools norm \ --fasta-ref Homo_sapiens_assembly38.fasta \ --output HD827.HD827-manta.generatesvcandidates 1.6.0.norm.vcf.gz \ -m -both -cw -Oz --write-index=tbi \ --threads 6 \ HD827.manta.diploid_sv.vcf.gz Command exit status: 255 Command output: (empty) Command error: [E::hts_open_format] Failed to open file "1.6.0.norm.vcf.gz" : No such file or directory Failed to read from 1.6.0.norm.vcf.gz: No such file or directory`

Relevant files

.nextflow.log.3.txt

System information

Nextflow 25.10.4
Local executor on a workstation.
Singularity
Ubuntu
ver 1.0.0