REHEADER gzip

[EladH1]

Description of the bug

The current version of REHEADER require vcf and not vcf.gz
also I believe the the test HG002_GRCh38_CMRG_smallvar_v1.00.vcf.gz you have is gunzip and not gzip.

I think you could repreduce this by

1. download the GIAB from https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/
   or

gunzip HG002_GRCh38_CMRG_smallvar_v1.00.vcf.gz
gzip HG002_GRCh38_CMRG_smallvar_v1.00.vcf

on commit of bcftools/reheader
https://github.com/nf-core/modules/commit/c32611ac6813055b9321d2827678e2f8aebcb394
they do

`
def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"

${create_cmd} ${prefix}.${extension}
`

not sure if this helps

`ERROR ~ Error executing process > 'NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:PREPARE_VCFS_TRUTH:VCF_REHEADER_SAMPLENAME:BCFTOOLS_REHEADER (GIAB-NA24385)'

Caused by:
Process NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:PREPARE_VCFS_TRUTH:VCF_REHEADER_SAMPLENAME:BCFTOOLS_REHEADER (GIAB-NA24385) terminated with an error exit status (255)

Command executed:

bcftools
reheader
--fai GRCh38_latest_genomic_final.fa.fai


--samples GIAB-NA24385.txt
--threads 2
HG002_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
| bcftools view
--output-type z
--output HG002_GRCh38_1_22_v4.2.1_benchmark.rh.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_VARIANTBENCHMARKING:VARIANTBENCHMARKING:PREPARE_VCFS_TRUTH:VCF_REHEADER_SAMPLENAME:BCFTOOLS_REHEADER":
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.bcftools //; s/ .$//')
END_VERSIONS

Command exit status:
255

Command output:
(empty)

Command error:
Error: cannot reheader gzip-compressed files, first convert with bcftools view --output-type to a supported format
Failed to read from standard input: unknown file type`

Command used and terminal output

Relevant files

No response

System information

No response

[kubranarci]

@EladH1 Hey, can you explain this further? I think this is not through one of test profiles? If that is the case, I would recommend to apply preprocesses before running the pipeline anyways. It is not easy to standardize preprocessing for each type..

[EladH1]

I can try..

if you 'file' on your TEST vcf you will see this":
file HG002.strelka.variants.chr21.vcf.gz
HG002.strelka.variants.chr21.vcf.gz: gzip compressed data, extra field

when I run it on my ref or the files of GIAB I don't see this extra field.
if you do
gunzip HG002.strelka.variants.chr21.vcf.gz
gzip HG002.strelka.variants.chr21.vcf

then, re-run I think you ill get the error I got :

"cannot reheader gzip-compressed files"

REHEADER had a change to introduce working with gzip...
but this is not in the current version.

[kubranarci]

I am updating bcftools reheader to 1.2 in this recent https://github.com/nf-core/variantbenchmarking/pull/128/files pull. But the problem is still not clear to me. Why changing truth GIAB vcfs will affect reheadering test vcfs.. Can you please add the full error files?