-
Notifications
You must be signed in to change notification settings - Fork 14
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Pipeline crashed when no variant is found #14
Comments
Do you have any example file to test this? |
If you use the tiny bed file on this test data set it will crash: git clone --depth=1 https://github.com/mfoll/NGS_data_test.git
cd NGS_data_test/1000G_CEU_TP53/
nextflow run mfoll/robust-regression-caller -with-docker mfoll/robust-regression-caller --bed \
TP53_tiny.bed --bam_folder BAM/ --fasta_ref 17.fasta.gz We can either:
|
@pditommaso suggestion:
|
That's complicating the pipeline just to produce an empty vcf output... I would rather prefer option 2 I mentioned above. |
As far as I'm understanding this happens only with the test data. Is it not possible to create a test dataset producing at least one entry in the vcf? |
No, it happened to me on real data and then I created a test replicating the issue. |
Thus, when the In my opinion for consistency it should create an empty pdf file (or none of them). |
Creates an empty pdf in all cases and delete them afterward
I am trying to delete the empty pdf files. But the empty pdf is only deleted when it is the only pdf produced. There must be an error in this line: https://github.com/mfoll/robust-regression-caller/blob/dev/samtools_regression_somatic_vcf.nf#L149 |
I'm a bit confused about that code. Why do you need a |
To copy it where I want it to be using |
Ok I was wrong, the |
Does it report an error message? what's the problem? |
No, but when the process |
If you want to replicate the issue you can use my test data: git clone --depth=1 https://github.com/mfoll/NGS_data_test.git
cd NGS_data_test/1000G_CEU_TP53/ Then: nextflow run mfoll/robust-regression-caller -with-docker mfoll/robust-regression-caller --bed TP53_tiny.bed --bam_folder BAM/ --fasta_ref 17.fasta.gz Creates the empty pdf and deletes it (absent from BAM/VCF). nextflow run mfoll/robust-regression-caller -with-docker mfoll/robust-regression-caller --bed TP53_exon2_11.bed --bam_folder BAM/ --fasta_ref 17.fasta.gz Creates the empty pdf and others, and then doesn't delete the empty one (present in BAM/VCF). |
OK, I think the problem is that when there's more than a pdf, the Said that, I've noticed that you have used |
Sorry @pditommaso I should have figured this out by myself (you should stop being so helpful, or users like me will become lazy!). It's working perfectly now. Yes I know the behaviour with |
It seems that when the process
R_regression
does not produce variants, as it does not produce pdf output (but theerrorStrategy 'ignore'
makes that acceptable), the empty vcf is not sent to the vcf channel:This creates an error in the
collect_vcf_result
process as there is no vcf there.The text was updated successfully, but these errors were encountered: