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vcf file from sv workflow have no header #118

Closed carolinehey closed 9 months ago

carolinehey commented 10 months ago

Is your feature related to a problem?

The vcf file cant be used in eg. IGV unless you include the CHROM header line (starting with one #)

Describe the solution you'd like

The header should be included by default

Describe alternatives you've considered

i have no alternatives

Additional context

No response

RenzoTale88 commented 10 months ago

Hi @carolinehey could you provide us with more details on the run? What components did you run, which VCF presents the issue, system details etc

carolinehey commented 10 months ago

Hei, This was my nextflow command: nextflow run epi2me-labs/wf-human-variation -r v1.8.2 -w /data/wf_hum_C -profile standard --phase_mod --cnv --sv --bin_size 50 -c /longread/resources/increase_memory.config --bam_min_coverage 1 --bam 112577795012_PAQ91410_ubam.bam --ref --ref /longread/resources/reference_genomes/GRCh38_Hg38/GRCh38_decoy_no_alt.fasta --sample_name 112577795012_PAQ91410_hg38 -resume.

It is the sv.vcf file that lack the header, but as far as i know it has never been there. None of our ealier produced vcf files form the sv workflow have it.
image

Let me know if you need more information.

RenzoTale88 commented 10 months ago

@carolinehey I think we need to reverse engineer the issue here. Would you mind sharing the .nextflow.log file you obtained from the workflow? From there on, we can try to figure out where things have gone wrong and why.

carolinehey commented 10 months ago

.nextflow.log

RenzoTale88 commented 10 months ago

Weird, I can't see any error in the log. Could you try rerunning the workflow using the latest version (v1.9.0) and let us know whether you encounter the same issue?

carolinehey commented 10 months ago

There is no error in the run. It has been running just fine except that the output file is missing an important component if you want to use it further. As far as i see the header (#CHROM) has never been there, not in newer runs and versions and not in older runs and versions. I actually just want you to include it :)

RenzoTale88 commented 10 months ago

@carolinehey would you be ok with running a test for me? Could you proceed as follow:

Clone the repository at the right version:

git clone -b v1.9.0 https://github.com/epi2me-labs/wf-human-variation

Replace the appropriate line:

sed -i 's/vcfsort/bcftools sort -m 2G -T .\/ -O v/g' wf-human-variation/modules/local/wf-human-sv.nf

Try running the new workflow

nextflow run ./wf-human-variation [OPTIONS HERE]
RenzoTale88 commented 10 months ago

@carolinehey I just realised a small mistake in one of the commands above. The second command should be:

sed -i 's/vcfsort/bcftools sort -m 2G -T .\/ -O v/g' wf-human-variation/modules/local/wf-human-sv.nf
RenzoTale88 commented 9 months ago

@carolinehey could you please try using v1.9.1

carolinehey commented 9 months ago

Sorry for the delay in response. I have tried some tests now and the SV workflow gives this error in the repport. image

RenzoTale88 commented 9 months ago

@carolinehey is this with v1.9.1 of the workflow?

carolinehey commented 9 months ago

Yes image

RenzoTale88 commented 9 months ago

Thanks for confirming this. Does the resulting VCF appears well formed this time? Or do you still have the missing header line?

carolinehey commented 9 months ago

There were no resulting VCF file due to the error i think

RenzoTale88 commented 9 months ago

Could you please check that the VCF file in here:

/data/wf_hum_var_work_E1/2b/43e78ca*/*.vcf.gz

Has the correct header?

carolinehey commented 9 months ago

I looks correct.

RenzoTale88 commented 9 months ago

Ok thanks for confirming this. I'll close this issue as fixed, and could you please open a new github issue with the details of this new error? Thanks in advance!