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Hi, Sorry for bothering you again! First, thanks!
I'm slowly pushing forward in running your pipeline, and have encountered the issues below:
1, as posted, the pipeline failed to install IEDB, due…
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Hi @tianshilu,
You uesd GATK3 in the somatic.pl,but now when I use GATK3, the RealignerTargetCreator, IndelRealigner and PrintReads function of GATK3 can not be found in my GATK3,may be GATK4 replace…
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User report:
I wanted to get functional annotation of variants identified in earlier steps of my analysis. I thought of using Funcotator for this purpose. Interestingly, the annotation differed from t…
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Hi!
I am very much interested and working over increasing scalability of GATK4 tool performances. There is explicit parameter setting for increased number of nodes over multi-node cluster. But curren…
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### Description of the bug
Then GATK4_BEDTOINTERVALLIST sometimes fails when using a variety of references genomes due to the incorrect creation of the genome.dict or exome.bed file from the refere…
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### Description of the bug
Running nf-core/rnavar:1.0.0 with genome references from igenome or user-specified fasta/gtf files will both encounter the following error when in the STAR_ALIGN stage:
…
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[//]: # (Please do not include your AWS account or credentials as part of the bug request.)
**Describe the Bug**
[//]: # (Please describe the behavior that you are seeing with as many details …
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### Description of the bug
This is the output that is seen on the terminal once the pipeline has failed after `GATK4_MARKDUPLICATES`, my guess is that one of the later join operator is causing the …
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### Description of the bug
The sarek pipeline repeatedly errors out at the GATK MarkDuplicates step with the message:
"Error occurred during initialization of VM
Could not reserve enough space …
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In the classic GATK, walkers had the option to be multi-thread in two different ways:
* `NanoSchedulable` for thread-safe `map()` calls.
* `TreeReducible` for thread-safe `map()` and `reduce()` ca…