I have the weird case that if I run ```nextflow run profile nf-core #nf-test

I have the weird case that if I run ```nextflow ru...

Famke Bäuerle

02/16/2026, 1:57 PM

I have the weird case that if I run

Copy code

nextflow run . -profile test,singularity ...

its works but if I run

Copy code

nf-test test --update-snapshot --profile=+test,singularity tests/default.nf.test

I get a java error:

Copy code

java.io.IOException: Unable to parse header with error: Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file, for input source: file:///home/paifb01/nf-core/variantprioritization/.nf-test/tests/c8e747fc7641104dbd75dabbcf1a0a0d/output/pcgr/HCC1395.HCC1395T/HCC1395.HCC1395T.pcgr.grch38.lxbmu0prglvqivf.vep.4qjzlj1el1.tmp.vcfanno.unsorted.vcf

that seems to be related to my module that creates these outputs but I do not understand why the error only happens when I run the pipeline via nf-test. Did someone experience something similar?

Niklas Schandry

02/16/2026, 2:00 PM

Is it maybe related to

nft-vcf

Niklas Schandry

02/16/2026, 2:01 PM

While I have poor understanding of the details (see my question above) I guess this plugin is loaded with

nf-test test

but not necessarily in your pipeline when running with

nextflow run

🫠 1

Famke Bäuerle

02/16/2026, 2:02 PM

good call that is most likely correct, let me investigate!

Famke Bäuerle

02/16/2026, 2:48 PM

@Niklas Schandry removing my vcf files from the output assertion did solve the issue indeed! thank you!

🙌 1

Open in Slack

Previous Next